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Ardelean MV, Kundnani NR, Sharma A, Dumitru M, Buzas R, Rosca CI, Dahdal D, Ottman N, Ardelean OF, Daniel-Marius DS, Stelian MI, Lighezan D. Fecal calprotectin - a valuable predictor of microscopic colitis. Eur Rev Med Pharmacol Sci 2022; 26:9382-9392. [PMID: 36591847 DOI: 10.26355/eurrev_202212_30689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVE Microscopic colitis (MC) has been of major concern worldwide due to its relapsing and remitting nature of chronic diarrhea. Quality of life of patients suffering from this disease is quite debilitating. PATIENTS AND METHODS In order to understand the role and importance of fecal calprotectin (FC) we performed a statistical analysis on the patients suffering from chronic diarrhea and admitted to our hospital from 2014 to 2020, and who were prescribed Loperamide (Imodium) or Budesonide or a combination of both and had undergone FC detection test. RESULTS FC was found to be significantly correlated to the age, alcohol consumption and beta blocker use. A high level of the FC concentrations increases the chances of having flare-ups of diarrhea episodes making the quality of life of such patients worse. CONCLUSIONS FC concentrations should be monitored frequently and precautionary measures to avoid a relapse should be aimed. Measures to improve quality of life, should be of prime concern. In-depth research is required to better understand MC and to find better treatment options which can be used on a long-term basis, instead of anti-motility drugs which are able to control the acute episodes, but when discontinued result in an increased tendency to have relapses.
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Affiliation(s)
- M V Ardelean
- Department of Internal Medicine I - Medical Semiology I, Advanced Research Center for Cardiovascular Pathology and Haemostaseology, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania.
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Lefèvre‐Utile A, Saichi M, Oláh P, Delord M, Homey B, Soumelis V, Kere J, Levi‐Schaffer F, Greco D, Ottman N, Baker J, Andersson B, Barrientos‐Somarribas M, Prast‐Nielsen S, Wisgrill L, Tsoka S, Fyhrquist N, Alenius H, Alexander H, Schröder JM, Nestle FO, Lauerma A, Hupé P, Ranki A. Transcriptome-based identification of novel endotypes in adult atopic dermatitis. Allergy 2022; 77:1486-1498. [PMID: 34689335 DOI: 10.1111/all.15150] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 04/12/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Atopic dermatitis (AD) is a frequent and heterogeneous inflammatory skin disease, for which personalized medicine remains a challenge. High-throughput approaches have improved understanding of the complex pathophysiology of AD. However, a purely data-driven AD classification is still lacking. METHODS To address this question, we applied an original unsupervised approach on the largest available transcriptome dataset of AD lesional (n = 82) and healthy (n = 213) skin biopsies. RESULTS Taking into account pathological and physiological state, a variance-based filtering revealed 222 AD-specific hyper-variable genes that efficiently classified the AD samples into 4 clusters that turned out to be clinically and biologically distinct. Comparison of gene expressions between clusters identified 3 sets of upregulated genes used to derive metagenes (MGs): MG-I (19 genes) was associated with IL-1 family signaling (including IL-36A and 36G) and skin remodeling, MG-II (23 genes) with negative immune regulation (including IL-34 and 37) and skin architecture, and MG-III (17 genes) with B lymphocyte immunity. Sample clusters differed in terms of disease severity (p = .02) and S. aureus (SA) colonization (p = .02). Cluster 1 contained the most severe AD, highest SA colonization, and overexpressed MG-I. Cluster 2 was characterized by less severe AD, low SA colonization, and high MG-II expression. Cluster 3 included mild AD, mild SA colonization, and mild expression of all MGs. Cluster 4 had the same clinical features as cluster 3 but had hyper-expression of MG-III. Last, we successfully validated our method and results in an independent cohort. CONCLUSION Our study revealed unrecognized AD endotypes with specific underlying biological pathways, highlighting novel pathophysiological mechanisms. These data could provide new insights into personalized treatment strategies.
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Affiliation(s)
- Alain Lefèvre‐Utile
- U976 HIPI Unit Institut de Recherche Saint‐Louis Université de Paris Inserm Paris France
- General Pediatrics and Pediatric Emergency Department Jean Verdier Hospital Assistance Publique‐Hôpitaux de Paris (APHP) Bondy France
- Université Paris Saclay Gif‐sur‐Yvette France
| | - Melissa Saichi
- U976 HIPI Unit Institut de Recherche Saint‐Louis Université de Paris Inserm Paris France
| | - Péter Oláh
- Department of Dermatology University of Duesseldorf Duesseldorf Germany
- Department of Dermatology, Venereology, and Oncodermatology Medical Faculty University of Pécs Pécs Hungary
| | - Marc Delord
- Clinical Research Center Centre Hospitalier de Versailles Le Chesnay France
| | - Bernhard Homey
- Department of Dermatology University of Duesseldorf Duesseldorf Germany
| | - Vassili Soumelis
- U976 HIPI Unit Institut de Recherche Saint‐Louis Université de Paris Inserm Paris France
- Laboratoire d'Immunologie et histocompatibilité Hôpital Saint‐Louis Assistance Publique‐Hôpitaux de Paris (AP‐HP) Paris France
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Riskumäki M, Tessas I, Ottman N, Suomalainen A, Werner P, Karisola P, Lauerma A, Ruokolainen L, Karkman A, Wisgrill L, Sinkko H, Lehtimäki J, Alenius H, Fyhrquist N. Interplay between skin microbiota and immunity in atopic individuals. Allergy 2021; 76:1280-1284. [PMID: 33480030 DOI: 10.1111/all.14744] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/18/2020] [Accepted: 01/18/2021] [Indexed: 12/21/2022]
Affiliation(s)
- Matilda Riskumäki
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Department of Bacteriology and Immunology Medicum University of Helsinki Helsinki Finland
| | - Ioannis Tessas
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | - Noora Ottman
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - Alina Suomalainen
- Department of Bacteriology and Immunology Medicum University of Helsinki Helsinki Finland
| | - Paulina Werner
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - Piia Karisola
- Department of Bacteriology and Immunology Medicum University of Helsinki Helsinki Finland
| | - Antti Lauerma
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | | | - Antti Karkman
- Department of Microbiology University of Helsinki Helsinki Finland
- Helsinki Institute of Sustainability Science (HELSUS) University of Helsinki Helsinki Finland
| | - Lukas Wisgrill
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Division of Neonatology Pediatric Intensive Care and Neuropediatrics Comprehensive Center for Pediatrics Medical University of Vienna Vienna Austria
| | - Hanna Sinkko
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Department of Bacteriology and Immunology Medicum University of Helsinki Helsinki Finland
| | | | - Harri Alenius
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Department of Bacteriology and Immunology Medicum University of Helsinki Helsinki Finland
| | - Nanna Fyhrquist
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Department of Bacteriology and Immunology Medicum University of Helsinki Helsinki Finland
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Ottman N, Barrientos‐Somarribas M, Fyhrquist N, Alexander H, Wisgrill L, Olah P, Tsoka S, Greco D, Levi‐Schaffer F, Soumelis V, Schröder JM, Kere J, Nestle FO, Barker J, Ranki A, Lauerma A, Homey B, Andersson B, Alenius H. Microbial and transcriptional differences elucidate atopic dermatitis heterogeneity across skin sites. Allergy 2021; 76:1173-1187. [PMID: 33001460 PMCID: PMC8246754 DOI: 10.1111/all.14606] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/03/2020] [Accepted: 09/06/2020] [Indexed: 12/29/2022]
Abstract
It is well established that different sites in healthy human skin are colonized by distinct microbial communities due to different physiological conditions. However, few studies have explored microbial heterogeneity between skin sites in diseased skin, such as atopic dermatitis (AD) lesions. To address this issue, we carried out deep analysis of the microbiome and transcriptome in the skin of a large cohort of AD patients and healthy volunteers, comparing two physiologically different sites: upper back and posterior thigh. Microbiome samples and biopsies were obtained from both lesional and nonlesional skin to identify changes related to the disease process. Transcriptome analysis revealed distinct disease-related gene expression profiles depending on anatomical location, with keratinization dominating the transcriptomic signatures in posterior thigh, and lipid metabolism in the upper back. Moreover, we show that relative abundance of Staphylococcus aureus is associated with disease severity in the posterior thigh, but not in the upper back. Our results suggest that AD may select for similar microbes in different anatomical locations-an "AD-like microbiome," but distinct microbial dynamics can still be observed when comparing posterior thigh to upper back. This study highlights the importance of considering the variability across skin sites when studying the development of skin inflammation.
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Affiliation(s)
- Noora Ottman
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | | | - Nanna Fyhrquist
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Human Microbiome Research Program University of Helsinki Helsinki Finland
| | - Helen Alexander
- St John's Institute of Dermatology Guy's and St Thomas' NHS Foundation Trust and King's College London London UK
| | - Lukas Wisgrill
- Division of Neonatology Pediatric Intensive Care and Neuropediatrics Medical University of Vienna Vienna Austria
| | - Peter Olah
- Department of Dermatology University Hospital Duesseldorf Duesseldorf Germany
- Department of Dermatology, Venereology and Oncodermatology University of Pécs Pécs Hungary
| | - Sophia Tsoka
- Department of Informatics Faculty of Natural and Mathematical Sciences King’s College London London UK
| | - Dario Greco
- Faculty of Medicine and Life Sciences University of Tampere Tampere Finland
- Institute of Biomedical Technology University of Tampere Tampere Finland
- Institute of Biotechnology University of Helsinki Helsinki Finland
| | - Francesca Levi‐Schaffer
- Pharmacology Unit School of Pharmacy Faculty of Medicine The Institute for Drug Research The Hebrew University of Jerusalem Jerusalem Israel
| | | | - Jens M. Schröder
- Department of Dermatology University Hospital Schleswig‐Holstein Kiel Germany
| | - Juha Kere
- Department of Biosciences and Nutrition Karolinska Institutet Stockholm Sweden
- School of Basic and Medical Biosciences King’s College London London UK
| | - Frank O. Nestle
- Cutaneous Medicine Unit St. John’s Institute of Dermatology and Biomedical Research Centre Faculty of Life Sciences and Medicine King’s College London London UK
| | - Jonathan Barker
- St John’s Institute of Dermatology Division of Genetics and Molecular Medicine Faculty of Life Sciences and Medicine Kings College London London UK
| | - Annamari Ranki
- Department of Dermatology, Allergology and Venereology Inflammation Centre University of Helsinki and Helsinki University Hospital Helsinki Finland
| | - Antti Lauerma
- Department of Dermatology, Allergology and Venereology Inflammation Centre University of Helsinki and Helsinki University Hospital Helsinki Finland
| | - Bernhard Homey
- Department of Dermatology University Hospital Duesseldorf Duesseldorf Germany
| | - Björn Andersson
- Department of Cell and Molecular Biology Karolinska Institutet Stockholm Sweden
| | - Harri Alenius
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Human Microbiome Research Program University of Helsinki Helsinki Finland
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5
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Ruokolainen L, Fyhrquist N, Laatikainen T, Auvinen P, Fortino V, Scala G, Jousilahti P, Karisola P, Vendelin J, Karkman A, Markelova O, Mäkelä MJ, Lehtimäki S, Ndika J, Ottman N, Paalanen L, Paulin L, Vartiainen E, von Hertzen L, Greco D, Haahtela T, Alenius H. Immune-microbiota interaction in Finnish and Russian Karelia young people with high and low allergy prevalence. Clin Exp Allergy 2020; 50:1148-1158. [PMID: 32865840 PMCID: PMC7589450 DOI: 10.1111/cea.13728] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022]
Abstract
Background After the Second World War, the population living in the Karelian region was strictly divided by the “iron curtain” between Finland and Russia. This resulted in different lifestyle, standard of living, and exposure to the environment. Allergic manifestations and sensitization to common allergens have been much more common on the Finnish compared to the Russian side. Objective The remarkable allergy disparity in the Finnish and Russian Karelia calls for immunological explanations. Methods Young people, aged 15‐20 years, in the Finnish (n = 69) and Russian (n = 75) Karelia were studied. The impact of genetic variation on the phenotype was studied by a genome‐wide association analysis. Differences in gene expression (transcriptome) were explored from the blood mononuclear cells (PBMC) and related to skin and nasal epithelium microbiota and sensitization. Results The genotype differences between the Finnish and Russian populations did not explain the allergy gap. The network of gene expression and skin and nasal microbiota was richer and more diverse in the Russian subjects. When the function of 261 differentially expressed genes was explored, innate immunity pathways were suppressed among Russians compared to Finns. Differences in the gene expression paralleled the microbiota disparity. High Acinetobacter abundance in Russians correlated with suppression of innate immune response. High‐total IgE was associated with enhanced anti‐viral response in the Finnish but not in the Russian subjects. Conclusions and clinical relevance Young populations living in the Finnish and Russian Karelia show marked differences in genome‐wide gene expression and host contrasting skin and nasal epithelium microbiota. The rich gene‐microbe network in Russians seems to result in a better‐balanced innate immunity and associates with low allergy prevalence.
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Affiliation(s)
- Lasse Ruokolainen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Nanna Fyhrquist
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Human Microbiome Research (HUMI), University of Helsinki, Helsinki, Finland
| | - Tiina Laatikainen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare (THL), Helsinki, Finland.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Giovanni Scala
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
| | - Pekka Jousilahti
- Department of Public Health Solutions, Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Piia Karisola
- Human Microbiome Research (HUMI), University of Helsinki, Helsinki, Finland
| | - Johanna Vendelin
- Unit of Systems Toxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Antti Karkman
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Mika J Mäkelä
- Skin and Allergy Hospital, Helsinki University Hospital & University of Helsinki, Helsinki, Finland
| | - Sari Lehtimäki
- HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Joseph Ndika
- Human Microbiome Research (HUMI), University of Helsinki, Helsinki, Finland
| | - Noora Ottman
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Laura Paalanen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Erkki Vartiainen
- Department of Public Health Solutions, Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Leena von Hertzen
- Skin and Allergy Hospital, Helsinki University Hospital & University of Helsinki, Helsinki, Finland
| | - Dario Greco
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Institute of Biomedical Technology, University of Tampere, Tampere, Finland.,Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital & University of Helsinki, Helsinki, Finland
| | - Harri Alenius
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Human Microbiome Research (HUMI), University of Helsinki, Helsinki, Finland
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Karisola P, Suomalainen A, Fortino V, Ottman N, Vendelin J, Wolff HJ, Ruokolainen L, Greco D, Fyhrquist N, Alenius H. Tape-stripping alters the microbe-host correlations in mouse skin. Allergy 2019; 74:617-621. [PMID: 30372529 DOI: 10.1111/all.13653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Piia Karisola
- Department of Bacteriology and Immunology; University of Helsinki; Helsinki Finland
| | - Alina Suomalainen
- Department of Bacteriology and Immunology; University of Helsinki; Helsinki Finland
| | - Vittorio Fortino
- Institute of Biomedicine; University of Eastern Finland; Kuopio Finland
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
- Institute of Biosciences and Medical Technologies; BioMediTech; University of Tampere; Tampere Finland
| | - Noora Ottman
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | | | | | | | - Dario Greco
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
- Institute of Biosciences and Medical Technologies; BioMediTech; University of Tampere; Tampere Finland
- Faculty of Medicine and Life Sciences; University of Tampere; Tampere Finland
| | - Nanna Fyhrquist
- Department of Bacteriology and Immunology; University of Helsinki; Helsinki Finland
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
| | - Harri Alenius
- Department of Bacteriology and Immunology; University of Helsinki; Helsinki Finland
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm Sweden
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Ottman N, Reunanen J, Meijerink M, Pietilä TE, Kainulainen V, Klievink J, Huuskonen L, Aalvink S, Skurnik M, Boeren S, Satokari R, Mercenier A, Palva A, Smidt H, de Vos WM, Belzer C. Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function. PLoS One 2017; 12:e0173004. [PMID: 28249045 PMCID: PMC5332112 DOI: 10.1371/journal.pone.0173004] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/12/2017] [Indexed: 12/24/2022] Open
Abstract
Gut barrier function is key in maintaining a balanced response between the host and its microbiome. The microbiota can modulate changes in gut barrier as well as metabolic and inflammatory responses. This highly complex system involves numerous microbiota-derived factors. The gut symbiont Akkermansia muciniphila is positively correlated with a lean phenotype, reduced body weight gain, amelioration of metabolic responses and restoration of gut barrier function by modulation of mucus layer thickness. However, the molecular mechanisms behind its metabolic and immunological regulatory properties are unexplored. Herein, we identify a highly abundant outer membrane pili-like protein of A. muciniphila MucT that is directly involved in immune regulation and enhancement of trans-epithelial resistance. The purified Amuc_1100 protein and enrichments containing all its associated proteins induced production of specific cytokines through activation of Toll-like receptor (TLR) 2 and TLR4. This mainly leads to high levels of IL-10 similar to those induced by the other beneficial immune suppressive microorganisms such as Faecalibacterium prausnitzii A2-165 and Lactobacillus plantarum WCFS1. Together these results indicate that outer membrane protein composition and particularly the newly identified highly abundant pili-like protein Amuc_1100 of A. muciniphila are involved in host immunological homeostasis at the gut mucosa, and improvement of gut barrier function.
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Affiliation(s)
- Noora Ottman
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Biosciences, University of Helsinki, Helsinki, Finland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Justus Reunanen
- Cancer and Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Marjolein Meijerink
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
- Department Risk Analysis for Products in Development, TNO, Zeist, the Netherlands
| | - Taija E. Pietilä
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Veera Kainulainen
- Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Judith Klievink
- Department of Bacteriology and Immunology, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, University of Helsinki and Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Laura Huuskonen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
- Helsinki University Central Hospital Laboratory Diagnostics, Helsinki, Finland
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Reetta Satokari
- Department of Bacteriology and Immunology, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Annick Mercenier
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Airi Palva
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Bacteriology and Immunology, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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Ottman N, Huuskonen L, Reunanen J, Boeren S, Klievink J, Smidt H, Belzer C, de Vos WM. Characterization of Outer Membrane Proteome of Akkermansia muciniphila Reveals Sets of Novel Proteins Exposed to the Human Intestine. Front Microbiol 2016; 7:1157. [PMID: 27507967 PMCID: PMC4960237 DOI: 10.3389/fmicb.2016.01157] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/12/2016] [Indexed: 12/26/2022] Open
Abstract
Akkermansia muciniphila is a common member of the human gut microbiota and belongs to the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum. Decreased levels of A. muciniphila have been associated with many diseases, and thus it is considered to be a beneficial resident of the intestinal mucus layer. Surface-exposed molecules produced by this organism likely play important roles in colonization and communication with other microbes and the host, but the protein composition of the outer membrane (OM) has not been characterized thus far. Herein we set out to identify and characterize A. muciniphila proteins using an integrated approach of proteomics and computational analysis. Sarkosyl extraction and sucrose density-gradient centrifugation methods were used to enrich and fractionate the OM proteome of A. muciniphila. Proteins from these fractions were identified by LC-MS/MS and candidates for OM proteins derived from the experimental approach were subjected to computational screening to verify their location in the cell. In total we identified 79 putative OM and membrane-associated extracellular proteins, and 23 of those were found to differ in abundance between cells of A. muciniphila grown on the natural substrate, mucin, and those grown on the non-mucus sugar, glucose. The identified OM proteins included highly abundant proteins involved in secretion and transport, as well as proteins predicted to take part in formation of the pili-like structures observed in A. muciniphila. The most abundant OM protein was a 95-kD protein, termed PilQ, annotated as a type IV pili secretin and predicted to be involved in the production of pili in A. muciniphila. To verify its location we purified the His-Tag labeled N-terminal domain of PilQ and generated rabbit polyclonal antibodies. Immunoelectron microscopy of thin sections immunolabeled with these antibodies demonstrated the OM localization of PilQ, testifying for its predicted function as a type IV pili secretin in A. muciniphila. As pili structures are known to be involved in the modulation of host immune responses, this provides support for the involvement of OM proteins in the host interaction of A. muciniphila. In conclusion, the characterization of A. muciniphila OM proteome provides valuable information that can be used for further functional and immunological studies.
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Affiliation(s)
- Noora Ottman
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands; Metapopulation Research Centre, University of HelsinkiHelsinki, Finland
| | - Laura Huuskonen
- Department of Veterinary Biosciences, University of Helsinki Helsinki, Finland
| | - Justus Reunanen
- Department of Veterinary Biosciences, University of HelsinkiHelsinki, Finland; Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of HelsinkiHelsinki, Finland
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University Wageningen, Netherlands
| | - Judith Klievink
- Immunobiology, Department of Bacteriology and Immunology, and Research Programs Unit, University of Helsinki Helsinki, Finland
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands; Department of Veterinary Biosciences, University of HelsinkiHelsinki, Finland; Immunobiology, Department of Bacteriology and Immunology, and Research Programs Unit, University of HelsinkiHelsinki, Finland
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9
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Ottman N, Smidt H, de Vos WM, Belzer C. The function of our microbiota: who is out there and what do they do? Front Cell Infect Microbiol 2012; 2:104. [PMID: 22919693 PMCID: PMC3417542 DOI: 10.3389/fcimb.2012.00104] [Citation(s) in RCA: 260] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 07/15/2012] [Indexed: 12/13/2022] Open
Abstract
Current meta-omics developments provide a portal into the functional potential and activity of the intestinal microbiota. The comparative and functional meta-omics approaches have made it possible to get a molecular snap shot of microbial function at a certain time and place. To this end, metagenomics is a DNA-based approach, metatranscriptomics studies the total transcribed RNA, metaproteomics focuses on protein levels and metabolomics describes metabolic profiles. Notably, the metagenomic toolbox is rapidly expanding and has been instrumental in the generation of draft genome sequences of over 1000 human associated microorganisms as well as an astonishing 3.3 million unique microbial genes derived from the intestinal tract of over 100 European adults. Remarkably, it appeared that there are at least 3 clusters of co-occurring microbial species, termed enterotypes, that characterize the intestinal microbiota throughout various continents. The human intestinal microbial metagenome further revealed unique functions carried out in the intestinal environment and provided the basis for newly discovered mechanisms for signaling, vitamin production and glycan, amino-acid and xenobiotic metabolism. The activity and composition of the microbiota is affected by genetic background, age, diet, and health status of the host. In its turn the microbiota composition and activity influence host metabolism and disease development. Exemplified by the differences in microbiota composition and activity between breast- as compared to formula-fed babies, healthy and malnourished infants, elderly and centenarians as compared to youngsters, humans that are either lean or obese and healthy or suffering of inflammatory bowel diseases (IBD). In this review we will focus on our current understanding of the functionality of the human intestinal microbiota based on all available metagenome, metatranscriptome, and metaproteome results
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Affiliation(s)
- Noora Ottman
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
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