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Sallam M, Mysara M, Benotmane MA, Tamarat R, Santos SCR, Crijns APG, Spoor D, Van Nieuwerburgh F, Deforce D, Baatout S, Guns PJ, Aerts A, Ramadan R. Correction: Sallam et al. DNA Methylation Alterations in Fractionally Irradiated Rats and Breast Cancer Patients Receiving Radiotherapy. Int. J. Mol. Sci. 2022, 23, 16214. Int J Mol Sci 2023; 24:17590. [PMID: 38139464 PMCID: PMC10743583 DOI: 10.3390/ijms242417590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 12/24/2023] Open
Abstract
Radia Tamarat and Susana Constantino Rosa Santos were not included as authors in the original publication [...].
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Affiliation(s)
- Magy Sallam
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
- Laboratory of Physiopharmacology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Mohamed Mysara
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | | | - Radia Tamarat
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PRP-HOM, SRBE, LR2I, 92260 Fontenay-aux-Roses, France
| | - Susana Constantino Rosa Santos
- Centro Cardiovascular da Universidade de Lisboa (CCUL@RISE), Lisbon School of Medicine of the Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Anne P. G. Crijns
- Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Daan Spoor
- Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
- Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Pieter-Jan Guns
- Laboratory of Physiopharmacology, University of Antwerp, 2610 Wilrijk, Belgium
| | - An Aerts
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - Raghda Ramadan
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
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2
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Horemans N, Kariuki J, Saenen E, Mysara M, Beemster GTS, Sprangers K, Pavlović I, Novak O, Van Hees M, Nauts R, Duarte GT, Cuypers A. Are Arabidopsis thaliana plants able to recover from exposure to gamma radiation? A molecular perspective. J Environ Radioact 2023; 270:107304. [PMID: 37871537 DOI: 10.1016/j.jenvrad.2023.107304] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/15/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023]
Abstract
Most plant research focuses on the responses immediately after exposure to ionizing irradiation (IR). However, it is as important to investigate how plants recover after exposure since this has a profound effect on future plant growth and development and hence on the long-term consequences of exposure to stress. This study aimed to investigate the IR-induced responses after exposure and during recovery by exposing 1-week old A. thaliana seedlings to gamma dose rates ranging from 27 to 103.7 mGy/h for 2 weeks and allowing them to recover for 4 days. A high-throughput RNAsequencing analysis was carried out. An enrichment of GO terms related to the metabolism of hormones was observed both after irradiation and during recovery at all dose rates. While plants exposed to the lowest dose rate activate defence responses after irradiation, they recover from the IR by resuming normal growth during the recovery period. Plants exposed to the intermediate dose rate invest in signalling and defence after irradiation. During recovery, in the plants exposed to the highest dose rate, fundamental metabolic processes such as photosynthesis and RNA modification were still affected. This might lead to detrimental effects in the long-term or in the next generations of those irradiated plants.
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Affiliation(s)
- Nele Horemans
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium.
| | - Jackline Kariuki
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium
| | - Eline Saenen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium
| | - Mohamed Mysara
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium
| | - Gerrit T S Beemster
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Katrien Sprangers
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Iva Pavlović
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Faculty of Science of Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Ondrej Novak
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences & Faculty of Science of Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - May Van Hees
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium
| | - Robin Nauts
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium
| | | | - Ann Cuypers
- Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium
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3
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Bassyouni M, Mysara M, Wohlers I, Busch H, Saber-Ayad M, El-Hadidi M. A comprehensive analysis of genetic risk for metabolic syndrome in the Egyptian population via allele frequency investigation and Missense3D predictions. Sci Rep 2023; 13:20517. [PMID: 37993469 PMCID: PMC10665412 DOI: 10.1038/s41598-023-46844-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Diabetes mellitus (DM) represents a major health problem in Egypt and worldwide, with increasing numbers of patients with prediabetes every year. Numerous factors, such as obesity, hyperlipidemia, and hypertension, which have recently become serious concerns, affect the complex pathophysiology of diabetes. These metabolic syndrome diseases are highly linked to genetic variability that drives certain populations, such as Egypt, to be more susceptible to developing DM. Here we conduct a comprehensive analysis to pinpoint the similarities and uniqueness among the Egyptian genome reference and the 1000-genome subpopulations (Europeans, Ad-Mixed Americans, South Asians, East Asians, and Africans), aiming at defining the potential genetic risk of metabolic syndromes. Selected approaches incorporated the analysis of the allele frequency of the different populations' variations, supported by genotypes' principal component analysis. Results show that the Egyptian's reference metabolic genes were clustered together with the Europeans', Ad-Mixed Americans', and South-Asians'. Additionally, 8563 variants were uniquely identified in the Egyptian cohort, from those, two were predicted to cause structural damage, namely, CDKAL1: 6_21065070 (A > T) and PPARG: 3_12351660 (C > T) utilizing the Missense3D database. The former is a protein coding gene associated with Type 2 DM while the latter is a key regulator of adipocyte differentiation and glucose homeostasis. Both variants were detected heterozygous in two different Egyptian individuals from overall 110 sample. This analysis sheds light on the unique genetic traits of the Egyptian population that play a role in the DM high prevalence in Egypt. The proposed analysis pipeline -available through GitHub- could be used to conduct similar analysis for other diseases across populations.
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Affiliation(s)
- Mahmoud Bassyouni
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
- Bioscience Research Laboratories Department, MARC for Medical Services and Scientific Research, 6th of October, Jiza, Egypt
| | - Mohamed Mysara
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
- Microbiology unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology, and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- Biomolecular Data Science in Pneumology, Research Center Borstel, 23845, Borstel, Germany
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology, and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Maha Saber-Ayad
- Department of Clinical Sciences, College of Medicine, University of Sharjah, 27272, Sharjah, UAE.
- Pharmacology Department, College of Medicine, Cairo University, Cairo, 12613, Egypt.
| | - Mohamed El-Hadidi
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt.
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham Dubai Campus, Dubai, United Arab Emirates.
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Van Dingenen L, Segers C, Wouters S, Mysara M, Leys N, Kumar-Singh S, Malhotra-Kumar S, Van Houdt R. Dissecting the role of the gut microbiome and fecal microbiota transplantation in radio- and immunotherapy treatment of colorectal cancer. Front Cell Infect Microbiol 2023; 13:1298264. [PMID: 38035338 PMCID: PMC10687483 DOI: 10.3389/fcimb.2023.1298264] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers and poses a major burden on the human health worldwide. At the moment, treatment of CRC consists of surgery in combination with (neo)adjuvant chemotherapy and/or radiotherapy. More recently, immune checkpoint blockers (ICBs) have also been approved for CRC treatment. In addition, recent studies have shown that radiotherapy and ICBs act synergistically, with radiotherapy stimulating the immune system that is activated by ICBs. However, both treatments are also associated with severe toxicity and efficacy issues, which can lead to temporary or permanent discontinuation of these treatment programs. There's growing evidence pointing to the gut microbiome playing a role in these issues. Some microorganisms seem to contribute to radiotherapy-associated toxicity and hinder ICB efficacy, while others seem to reduce radiotherapy-associated toxicity or enhance ICB efficacy. Consequently, fecal microbiota transplantation (FMT) has been applied to reduce radio- and immunotherapy-related toxicity and enhance their efficacies. Here, we have reviewed the currently available preclinical and clinical data in CRC treatment, with a focus on how the gut microbiome influences radio- and immunotherapy toxicity and efficacy and if these treatments could benefit from FMT.
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Affiliation(s)
- Lena Van Dingenen
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Charlotte Segers
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Shari Wouters
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Mohamed Mysara
- Bioinformatics Group, Center for Informatics Science, School of Information Technology and Computer Science, Nile University, Giza, Egypt
| | - Natalie Leys
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Samir Kumar-Singh
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Rob Van Houdt
- Nuclear Medical Applications, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
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5
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Acchioni C, Acchioni M, Mancini F, Amendola A, Marsili G, Tirelli V, Gwee CP, Chan KWK, Sandini S, Bisbocci M, Mysara M, ElHefnawi M, Sanchez M, Venturi G, Barreca ML, Manfroni G, Bresciani A, Vasudevan SG, Sgarbanti M. A cellular screening platform, stably expressing DENV2 NS5, defines a novel anti-DENV mechanism of action of Apigenin based on STAT2 activation. Virology 2023; 583:1-13. [PMID: 37060797 DOI: 10.1016/j.virol.2023.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 04/17/2023]
Abstract
Type I interferon (IFN-I) evasion by Dengue virus (DENV) is key in DENV pathogenesis. The non-structural protein 5 (NS5) antagonizes IFN-I response through the degradation of the signal transducer and activator of transcription 2 (STAT2). We developed a K562 cell-based platform, for high throughput screening of compounds potentially counteracting the NS5-mediated antagonism of IFN-I signaling. Upon a screening with a library of 1220 approved drugs, 3 compounds previously linked to DENV inhibition (Apigenin, Chrysin, and Luteolin) were identified. Luteolin and Apigenin determined a significant inhibition of DENV2 replication in Huh7 cells and the restoration of STAT2 phosphorylation in both cell systems. Apigenin and Luteolin were able to stimulate STAT2 even in the absence of infection. Despite the "promiscuous" and "pan-assay-interfering" nature of Luteolin, Apigenin promotes STAT2 Tyr 689 phosphorylation and activation, highlighting the importance of screening for compounds able to interact with host factors, to counteract viral proteins capable of dampening innate immune responses.
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Affiliation(s)
- Chiara Acchioni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Marta Acchioni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Flavia Mancini
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Antonello Amendola
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Giulia Marsili
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Valentina Tirelli
- Core Facility Service, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Chin Piaw Gwee
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road, 169857, Singapore.
| | - Kitti Wing-Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road, 169857, Singapore.
| | - Silvia Sandini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Monica Bisbocci
- Department of Translational and Discovery Research, IRBM S.p.A., Pomezia, Roma, Italy.
| | - Mohamed Mysara
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt.
| | - Mahmoud ElHefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt.
| | - Massimo Sanchez
- Core Facility Service, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Giulietta Venturi
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, Università Degli Studi di Perugia, Via Del Liceo 1, 06123, Perugia, Italy.
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, Università Degli Studi di Perugia, Via Del Liceo 1, 06123, Perugia, Italy.
| | - Alberto Bresciani
- Department of Translational and Discovery Research, IRBM S.p.A., Pomezia, Roma, Italy
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8-College Road, 169857, Singapore.
| | - Marco Sgarbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
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6
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Segers C, Mysara M, Coolkens A, Wouters S, Baatout S, Leys N, Lebeer S, Verslegers M, Mastroleo F. Limnospira indica PCC 8005 Supplementation Prevents Pelvic Irradiation-Induced Dysbiosis but Not Acute Inflammation in Mice. Antioxidants (Basel) 2023; 12:antiox12030572. [PMID: 36978820 PMCID: PMC10045453 DOI: 10.3390/antiox12030572] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Pelvic irradiation-induced mucositis secondarily leads to dysbiosis, which seriously affects patients’ quality of life after treatment. No safe and effective radioprotector or mitigator has yet been approved for clinical therapy. Here, we investigated the potential protective effects of fresh biomass of Limnospira indica PCC 8005 against ionizing irradiation-induced mucositis and dysbiosis in respect to benchmark probiotic Lacticaseibacillus rhamnosus GG ATCC 53103. For this, mice were supplemented daily before and after 12 Gy X-irradiation of the pelvis. Upon sacrifice, food supplements’ efficacy was assessed for intestinal barrier protection, immunomodulation and changes in the microbiota composition. While both could not confer barrier protection or significant immunomodulatory effects, 16S microbial profiling revealed that L. indica PCC 8005 and L. rhamnosus GG could prevent pelvic irradiation-induced dysbiosis. Altogether, our data show that—besides benchmarked L. rhamnosus GG—L. indica PCC 8005 is an interesting candidate to further explore as a radiomitigator counteracting pelvic irradiation-induced dysbiosis in the presented in vivo irradiation–gut–microbiota platform.
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Affiliation(s)
- Charlotte Segers
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
- Department of Bioscience Engineering, University of Antwerp, 2020 Antwerp, Belgium
| | - Mohamed Mysara
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - Amelie Coolkens
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - Shari Wouters
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - Sarah Baatout
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - Natalie Leys
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, 2020 Antwerp, Belgium
| | - Mieke Verslegers
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - Felice Mastroleo
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
- Correspondence: ; Tel.: +32-14-33-23-88
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7
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Van Antro M, Prelovsek S, Ivanovic S, Gawehns F, Wagemaker NCAM, Mysara M, Horemans N, Vergeer P, Verhoeven KJF. DNA methylation in clonal duckweed (Lemna minor L.) lineages reflects current and historical environmental exposures. Mol Ecol 2023; 32:428-443. [PMID: 36324253 PMCID: PMC10100429 DOI: 10.1111/mec.16757] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 09/16/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
Environmentally induced DNA methylation variants may mediate gene expression responses to environmental changes. If such induced variants are transgenerationally stable, there is potential for expression responses to persist over multiple generations. Our current knowledge in plants, however, is almost exclusively based on studies conducted in sexually reproducing species where the majority of DNA methylation changes are subject to resetting in germlines, limiting the potential for transgenerational epigenetics stress memory. Asexual reproduction circumvents germlines, and may therefore be more conducive to long-term inheritance of epigenetic marks. Taking advantage of the rapid clonal reproduction of the common duckweed Lemna minor, we hypothesize that long-term, transgenerational stress memory from exposure to high temperature can be detected in DNA methylation profiles. Using a reduced representation bisulphite sequencing approach (epiGBS), we show that temperature stress induces DNA hypermethylation at many CG and CHG cytosine contexts but not CHH. Additionally, differential methylation in CHG context that was observed was still detected in a subset of cytosines, even after 3-12 generations of culturing in a common environment. This demonstrates a memory effect of stress reflected in the methylome and that persists over multiple clonal generations. Structural annotation revealed that this memory effect in CHG methylation was enriched in transposable elements. The observed epigenetic stress memory is probably caused by stable transgenerational persistence of temperature-induced DNA methylation variants across clonal generations. To the extent that such epigenetic memory has functional consequences for gene expression and phenotypes, this result suggests potential for long-term modulation of stress responses in asexual plants.
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Affiliation(s)
- Morgane Van Antro
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Stella Prelovsek
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Slavica Ivanovic
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Fleur Gawehns
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Mohamed Mysara
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Nele Horemans
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Philippine Vergeer
- Plant Ecology and Physiology, Radboud University, Nijmegen, The Netherlands.,Wageningen University and Research (WUR), Plant Ecology and Nature Conservation Group, Wageningen, The Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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8
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Sallam M, Mysara M, Benotmane MA, Crijns APG, Spoor D, Van Nieuwerburgh F, Deforce D, Baatout S, Guns PJ, Aerts A, Ramadan R. DNA Methylation Alterations in Fractionally Irradiated Rats and Breast Cancer Patients Receiving Radiotherapy. Int J Mol Sci 2022; 23:16214. [PMID: 36555856 PMCID: PMC9783664 DOI: 10.3390/ijms232416214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Radiation-Induced CardioVascular Disease (RICVD) is an important concern in thoracic radiotherapy with complex underlying pathophysiology. Recently, we proposed DNA methylation as a possible mechanism contributing to RICVD. The current study investigates DNA methylation in heart-irradiated rats and radiotherapy-treated breast cancer (BC) patients. Rats received fractionated whole heart X-irradiation (0, 0.92, 6.9 and 27.6 Gy total doses) and blood was collected after 1.5, 3, 7 and 12 months. Global and gene-specific methylation of the samples were evaluated; and gene expression of selected differentially methylated regions (DMRs) was validated in rat and BC patient blood. In rats receiving an absorbed dose of 27.6 Gy, DNA methylation alterations were detected up to 7 months with differential expression of cardiac-relevant DMRs. Of those, SLMAP showed increased expression at 1.5 months, which correlated with hypomethylation. Furthermore, E2F6 inversely correlated with a decreased global longitudinal strain. In BC patients, E2F6 and SLMAP exhibited differential expression directly and 6 months after radiotherapy, respectively. This study describes a systemic radiation fingerprint at the DNA methylation level, elucidating a possible association of DNA methylation to RICVD pathophysiology, to be validated in future mechanistic studies.
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Affiliation(s)
- Magy Sallam
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
- Laboratory of Physiopharmacology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Mohamed Mysara
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | | | - Anne P. G. Crijns
- Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Daan Spoor
- Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
- Department of Molecular Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Pieter-Jan Guns
- Laboratory of Physiopharmacology, University of Antwerp, 2610 Wilrijk, Belgium
| | - An Aerts
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
| | - Raghda Ramadan
- Radiobiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, 2400 Mol, Belgium
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9
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Goussarov G, Mysara M, Vandamme P, Van Houdt R. Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data. Microbiologyopen 2022; 11:e1298. [PMID: 35765182 PMCID: PMC9179125 DOI: 10.1002/mbo3.1298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
The rise of metagenomics offers a leap forward for understanding the genetic diversity of microorganisms in many different complex environments by providing a platform that can identify potentially unlimited numbers of known and novel microorganisms. As such, it is impossible to imagine new major initiatives without metagenomics. Nevertheless, it represents a relatively new discipline with various levels of complexity and demands on bioinformatics. The underlying principles and methods used in metagenomics are often seen as common knowledge and often not detailed or fragmented. Therefore, we reviewed these to guide microbiologists in taking the first steps into metagenomics. We specifically focus on a workflow aimed at reconstructing individual genomes, that is, metagenome‐assembled genomes, integrating DNA sequencing, assembly, binning, identification and annotation.
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Affiliation(s)
- Gleb Goussarov
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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10
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Van Averbeke V, Berkell M, Mysara M, Rodriguez-Ruiz JP, Xavier BB, De Winter FHR, Jongers B', Jairam RK, Hotterbeekx A, Goossens H, Cohen ES, Malhotra-Kumar S, Kumar-Singh S. Host Immunity Influences the Composition of Murine Gut Microbiota. Front Immunol 2022; 13:828016. [PMID: 35371073 PMCID: PMC8965567 DOI: 10.3389/fimmu.2022.828016] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/21/2022] [Indexed: 12/24/2022] Open
Abstract
The influence of gut microbiota on host immunity is widely studied, and its disturbance has been linked to several immune-mediated disorders. Conversely, whether and how inherently disturbed canonical Th1 (pro-inflammatory) and/or Th2 (anti-inflammatory) immune pathways modify the host microbiome is not sufficiently investigated. Here, we characterized the humoral, cellular, and cytokine immunity, and associated alterations in gut microbiota of naïve wild-type mice (C57BL/6 and BALB/c), and mice with deficiencies in Th2 responses (IL-4Rα and IL-33 knockout mice) or in both Th1 and Th2 responses (NOD scid gamma, NSG mice). A global analysis by de novo clustering of 16S rRNA profiles of the gut microbiota independently grouped wild-type immunocompetent (C57BL/6 and BALB/c), Th2-deficient (IL-4Rα-/- and IL-33-/-), and severely immunodeficient (NSG) mice; where wild-type mice, but not Th2 or severely immunodeficient mice, were enriched in gut bacteria that produce short-chain fatty acids. These include members of phyla Firmicutes, Verrucomicrobia, and Bacteroidetes such as Lactobacillus spp., Akkermansia muciniphila, and Odoribacter spp. Further comparison of the two naïve wild-type mouse strains showed higher microbial diversity (Shannon), primarily linked to higher richness (Chao1), as well as a distinct difference in microbial composition (weighted UniFrac) in BALB/c mice compared to C57BL/6. T-cell and blood cytokine analyses demonstrated a Th1-polarization in naïve adaptive immunity in C57BL/6 animals compared to BALB/c mice, and an expected Th2 deficient cellular response in IL-4Rα-/- and IL-33-/- mice compared to its genetic background BALB/c strain. Together, these data suggest that alterations in the Th1/Th2 balance or a complete ablation of Th1/Th2 responses can lead to major alterations in gut microbiota composition and function. Given the similarities between the human and mouse immune systems and gut microbiota, our finding that immune status is a strong driver of gut microbiota composition has important consequences for human immunodeficiency studies.
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Affiliation(s)
- Vincent Van Averbeke
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Matilda Berkell
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium.,Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK-CEN), Mol, Belgium
| | - Juan Pablo Rodriguez-Ruiz
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Fien H R De Winter
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Bart 's Jongers
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Ravi Kumar Jairam
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - An Hotterbeekx
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - E Suzanne Cohen
- Bioscience Asthma, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Samir Kumar-Singh
- Molecular Pathology Group, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium.,Laboratory of Medical Microbiology - Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.,Translational Neurosciences, University of Antwerp, Antwerp, Belgium
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11
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Goussarov G, Claesen J, Mysara M, Cleenwerck I, Leys N, Vandamme P, Van Houdt R. Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics. Environ Microbiome 2022; 17:9. [PMID: 35248155 PMCID: PMC8898458 DOI: 10.1186/s40793-022-00403-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/17/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Although the total number of microbial taxa on Earth is under debate, it is clear that only a small fraction of these has been cultivated and validly named. Evidently, the inability to culture most bacteria outside of very specific conditions severely limits their characterization and further studies. In the last decade, a major part of the solution to this problem has been the use of metagenome sequencing, whereby the DNA of an entire microbial community is sequenced, followed by the in silico reconstruction of genomes of its novel component species. The large discrepancy between the number of sequenced type strain genomes (around 12,000) and total microbial diversity (106-1012 species) directs these efforts to de novo assembly and binning. Unfortunately, these steps are error-prone and as such, the results have to be intensely scrutinized to avoid publishing incomplete and low-quality genomes. RESULTS We developed MAGISTA (metagenome-assembled genome intra-bin statistics assessment), a novel approach to assess metagenome-assembled genome quality that tackles some of the often-neglected drawbacks of current reference gene-based methods. MAGISTA is based on alignment-free distance distributions between contig fragments within metagenomic bins, rather than a set of reference genes. For proper training, a highly complex genomic DNA mock community was needed and constructed by pooling genomic DNA of 227 bacterial strains, specifically selected to obtain a wide variety representing the major phylogenetic lineages of cultivable bacteria. CONCLUSIONS MAGISTA achieved a 20% reduction in root-mean-square error in comparison to the marker gene approach when tested on publicly available mock metagenomes. Furthermore, our highly complex genomic DNA mock community is a very valuable tool for benchmarking (new) metagenome analysis methods.
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Affiliation(s)
- Gleb Goussarov
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Jürgen Claesen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Department of Epidemiology & Biostatistics, Amsterdam UMC, VU University, Amsterdam, The Netherlands
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Ilse Cleenwerck
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.
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12
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Ruan JL, Lee C, Wouters S, Tullis IDC, Verslegers M, Mysara M, Then CK, Smart SC, Hill MA, Muschel RJ, Giaccia AJ, Vojnovic B, Kiltie AE, Petersson K. Irradiation at Ultra-High (FLASH) Dose Rates Reduces Acute Normal Tissue Toxicity in the Mouse Gastrointestinal System. Int J Radiat Oncol Biol Phys 2021; 111:1250-1261. [PMID: 34400268 PMCID: PMC7612009 DOI: 10.1016/j.ijrobp.2021.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE Preclinical studies using ultra-high dose rate (FLASH) irradiation have demonstrated reduced normal tissue toxicity compared with conventional dose rate (CONV) irradiation, although this finding is not universal. We investigated the effect of temporal pulse structure and average dose rate of FLASH compared with CONV irradiation on acute intestinal toxicity. MATERIALS AND METHODS Whole abdomens of C3H mice were irradiated with a single fraction to various doses, using a 6 MeV electron linear accelerator with single pulse FLASH (dose rate = 2-6 × 106 Gy/s) or conventional (CONV; 0.25 Gy/s) irradiation. At 3.75 days postirradiation, fresh feces were collected for 16S rRNA sequencing to assess changes in the gut microbiota. A Swiss roll-based crypt assay was used to quantify acute damage to the intestinal crypts to determine how tissue toxicity was affected by the different temporal pulse structures of FLASH delivery. RESULTS We found statistically significant improvements in crypt survival for mice irradiated with FLASH at doses between 7.5 and 12.5 Gy, with a dose modifying factor of 1.1 for FLASH (7.5 Gy, P < .01; 10 Gy, P < .05; 12.5 Gy, P < .01). This sparing effect was lost when the delivery time was increased, either by increasing the number of irradiation pulses or by prolonging the time between 2 successive pulses. Sparing was observed for average dose rates of ≥280 Gy/s. Fecal microbiome analysis showed that FLASH irradiation caused fewer changes to the microbiota than CONV irradiation. CONCLUSIONS This study demonstrates that FLASH irradiation can spare mouse small intestinal crypts and reduce changes in gut microbiome composition compared with CONV irradiation. The higher the average dose rate, the larger the FLASH effect, which is also influenced by temporal pulse structure of the delivery.
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Affiliation(s)
- Jia-Ling Ruan
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, United Kingdom
| | - Carl Lee
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, United Kingdom
| | - Shari Wouters
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Center (SCK CEN), Mol, Belgium; Molecular Pathology Group, Cell Biology and Histology and Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Campus Drie Eiken, University of Antwerp, Antwerp, Belgium
| | - Iain D C Tullis
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, United Kingdom
| | - Mieke Verslegers
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Center (SCK CEN), Mol, Belgium
| | - Mohamed Mysara
- Interdisciplinary Biosciences Group, Belgian Nuclear Research Center (SCK CEN), Mol, Belgium
| | - Chee Kin Then
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, United Kingdom
| | - Sean C Smart
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, United Kingdom
| | - Mark A Hill
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, United Kingdom
| | - Ruth J Muschel
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, United Kingdom
| | - Amato J Giaccia
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, United Kingdom
| | - Borivoj Vojnovic
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, United Kingdom
| | - Anne E Kiltie
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, United Kingdom
| | - Kristoffer Petersson
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, United Kingdom; Radiation Physics, Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden.
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13
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Van Eesbeeck V, Props R, Mysara M, Petit PCM, Rivasseau C, Armengaud J, Monsieurs P, Mahillon J, Leys N. Cyclical Patterns Affect Microbial Dynamics in the Water Basin of a Nuclear Research Reactor. Front Microbiol 2021; 12:744115. [PMID: 34721343 PMCID: PMC8555696 DOI: 10.3389/fmicb.2021.744115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
The BR2 nuclear research reactor in Mol, Belgium, runs in successive phases of operation (cycles) and shutdown, whereby a water basin surrounding the reactor vessel undergoes periodic changes in physico-chemical parameters such as flow rate, temperature, and radiation. The aim of this study was to explore the microbial community in this unique environment and to investigate its long-term dynamics using a 16S rRNA amplicon sequencing approach. Results from two sampling campaigns spanning several months showed a clear shift in community profiles: cycles were mostly dominated by two Operational Taxonomic Units (OTUs) assigned to unclassified Gammaproteobacterium and Pelomonas, whereas shutdowns were dominated by an OTU assigned to Methylobacterium. Although 1 year apart, both campaigns showed similar results, indicating that the system remained stable over this 2-year period. The community shifts were linked with changes in physico-chemical parameters by Non-metric Multidimensional Scaling (NMDS) and correlation analyses. In addition, radiation was hypothesized to cause a decrease in cell number, whereas temperature had the opposite effect. Chemoautotrophic use of H2 and dead cell recycling are proposed to be used as a strategies for nutrient retrieval in this extremely oligotrophic environment.
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Affiliation(s)
- Valérie Van Eesbeeck
- Microbiology Unit, Environment, Health and Safety Department, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Food and Environmental Microbiology Laboratory, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Ruben Props
- Microbiology Unit, Environment, Health and Safety Department, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Environment, Health and Safety Department, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Pauline C M Petit
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Paris, France
| | - Corinne Rivasseau
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Paris, France
| | - Jean Armengaud
- Technological Innovations for Detection and Diagnosis Laboratory, CEA, Bagnols-sur-Cèze, France
| | - Pieter Monsieurs
- Protozoology Research Group, Department of Biomedical Sciences, Institute of Tropical Medicine (ITG), Antwerp, Belgium
| | - Jacques Mahillon
- Food and Environmental Microbiology Laboratory, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Natalie Leys
- Microbiology Unit, Environment, Health and Safety Department, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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14
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Mysara M, Berkell M, Xavier BB, De Backer S, Lammens C, Hautekiet V, Petkov S, Goossens H, Kumar-Singh S, Malhotra-Kumar S. Assessing the Impact of Flavophospholipol and Virginiamycin Supplementation on the Broiler Microbiota: a Prospective Controlled Intervention Study. mSystems 2021; 6:e0038121. [PMID: 34463581 DOI: 10.1128/msystems.00381-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/02/2021] [Indexed: 12/13/2022] Open
Abstract
The antibiotic growth promoters (AGPs) flavophospholipol and virginiamycin have been widely used for decades in food animal production. AGP activity is believed to be partly modulated by gut microbial composition although exact AGP-induced changes remain unclear. In a controlled intervention study, we studied the effect of flavophospholipol and virginiamycin on the broiler chicken ileal microbiota spanning from birth to 39 days. Using 16S rRNA gene profiling and prediction of metabolic activity, we show that both AGPs result in dynamic microbial shifts that potentially increase anti-inflammatory mechanisms and bioavailability of several essential nutrients by decreasing degradation (flavophospholipol) or increasing biosynthesis (virginiamycin). Further, virginiamycin-supplemented broilers showed increased colonization with potentially pathogenic bacteria, Clostridium perfringens, Campylobacter, and Escherichia/Shigella spp. Overall, we show that both AGPs induce microbial changes potentially beneficial for growth. However, the increase in (foodborne) pathogens shown here with virginiamycin use could impact not only broiler mortality but also human health. IMPORTANCE Antibiotic growth promoters (AGPs) are commonly used within poultry farming to increase muscle growth. Microbial composition in the gut is known to be influenced by AGP use although exact AGP-induced changes remain unclear. Utilizing 16S rRNA gene profiling, this study provides a first head-to-head comparison of the effect of the two most commonly used AGPs, flavophospholipol and virginiamycin, on the broiler chicken ileum microbiota over time. We found that supplementation with both AGPs altered ileal microbial composition, thereby increasing potential bioavailability of essential nutrients and weight gain. Flavophospholipol showed a slight benefit over virginiamycin as the latter resulted in more extensive microbial perturbations including increased colonization by enteropathogens, which could impact broiler mortality.
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Affiliation(s)
- Mohamed Mysara
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centregrid.8953.7, SCK•CEN, Mol, Belgium
| | - Matilda Berkell
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
- Molecular Pathology group, Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | - Basil Britto Xavier
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | - Sarah De Backer
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | - Christine Lammens
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | | | | | - Herman Goossens
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | - Samir Kumar-Singh
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
- Molecular Pathology group, Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerpgrid.5284.b, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Lab of Medical Microbiology, Faculty of Medicine and Health Sciences, Vaccine & Infectious Disease Institute, University of Antwerpgrid.5284.b, Antwerp, Belgium
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15
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Yadav A, Maertens L, Meese T, Van Nieuwerburgh F, Mysara M, Leys N, Cuypers A, Janssen PJ. Genetic Responses of Metabolically Active Limnospira indica Strain PCC 8005 Exposed to γ-Radiation during Its Lifecycle. Microorganisms 2021; 9:microorganisms9081626. [PMID: 34442705 PMCID: PMC8400943 DOI: 10.3390/microorganisms9081626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
Two morphotypes of the cyanobacterial Limnospira indica (formerly Arthrospira sp.) strain PCC 8005, denoted as P2 (straight trichomes) and P6 (helical trichomes), were subjected to chronic gamma radiation from spent nuclear fuel (SNF) rods at a dose rate of ca. 80 Gy·h-1 for one mass doubling period (approximately 3 days) under continuous light with photoautotrophic metabolism fully active. Samples were taken for post-irradiation growth recovery and RNA-Seq transcriptional analysis at time intervals of 15, 40, and 71.5 h corresponding to cumulative doses of ca. 1450, 3200, and 5700 Gy, respectively. Both morphotypes, which were previously reported by us to display different antioxidant capacities and differ at the genomic level in 168 SNPs, 48 indels and 4 large insertions, recovered equally well from 1450 and 3200 Gy. However, while the P2 straight type recovered from 5700 Gy by regaining normal growth within 6 days, the P6 helical type took about 13 days to recover from this dose, indicating differences in their radiation tolerance and response. To investigate these differences, P2 and P6 cells exposed to the intermediate dose of gamma radiation (3200 Gy) were analyzed for differential gene expression by RNA-Seq analysis. Prior to batch normalization, a total of 1553 genes (887 and 666 of P2 and P6, respectively, with 352 genes in common) were selected based on a two-fold change in expression and a false discovery rate FDR smaller or equal to 0.05. About 85% of these 1553 genes encoded products of yet unknown function. Of the 229 remaining genes, 171 had a defined function while 58 genes were transcribed into non-coding RNA including 21 tRNAs (all downregulated). Batch normalization resulted in 660 differentially expressed genes with 98 having a function and 32 encoding RNA. From PCC 8005-P2 and PCC 8005-P6 expression patterns, it emerges that although the cellular routes used by the two substrains to cope with ionizing radiation do overlap to a large extent, both strains displayed a distinct preference of priorities.
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Affiliation(s)
- Anu Yadav
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium;
| | - Laurens Maertens
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
- Research Unit in Biology of Microorganisms (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium
| | - Tim Meese
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium; (T.M.); (F.V.N.)
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium; (T.M.); (F.V.N.)
| | - Mohamed Mysara
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
| | - Natalie Leys
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
| | - Ann Cuypers
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium;
| | - Paul Jaak Janssen
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
- Correspondence: ; Tel.: +32-14-332-129
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16
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Miloud SB, Dziri O, Ferjani S, Ali MM, Mysara M, Boutiba I, Houdt RVAN, Chouchani C. First Description of Various Bacteria Resistant to Heavy Metals and Antibiotics Isolated from Polluted Sites in Tunisia. Pol J Microbiol 2021; 70:161-174. [PMID: 34335797 PMCID: PMC8318066 DOI: 10.33073/pjm-2021-012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 01/11/2023] Open
Abstract
Environmental bacteria belonging to various families were isolated from polluted water collected from ten different sites in Tunisia. Sites were chosen near industrial and urban areas known for their high degree of pollution. The aim of this study was to investigate cross-resistance between heavy metals (HM), i.e., silver, mercury and copper (Ag, Hg, and Cu), and antibiotics. In an initial screening, 80 isolates were selected on ampicillin, and 39 isolates, retained for further analysis, could grow on a Tris-buffered mineral medium with gluconate as carbon source. Isolates were identified based on their 16S rRNA gene sequence. Results showed the prevalence of antibiotic resistance genes, especially all isolates harbored the blaTEM gene. Some of them (15.38%) harbored blaSHV. Moreover, several were even ESBLs and MBLs-producers, which can threaten the human health. On the other hand, 92.30%, 56.41%, and 51.28% of the isolates harbored the heavy metals resistance genes silE, cusA, and merA, respectively. These genes confer resistance to silver, copper, and mercury. A cross-resistance between antibiotics and heavy metals was detected in 97.43% of our isolates.
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Affiliation(s)
- Samar Ben Miloud
- Research Laboratory of Environmental Sciences and Technologies, Higher Institute of Environmental Sciences and Technologies of Borj-Cedria, University of Carthage, Hammam-Lif, Tunisia.,Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis El-Manar, Tunisia.,Research Laboratory Antibiotic Resistance, Faculty of Medicine of Tunis, Tunisia
| | - Olfa Dziri
- Research Laboratory of Environmental Sciences and Technologies, Higher Institute of Environmental Sciences and Technologies of Borj-Cedria, University of Carthage, Hammam-Lif, Tunisia.,Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis El-Manar, Tunisia
| | - Sana Ferjani
- Research Laboratory Antibiotic Resistance, Faculty of Medicine of Tunis, Tunisia
| | - Muntasir Md Ali
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Ilhem Boutiba
- Research Laboratory Antibiotic Resistance, Faculty of Medicine of Tunis, Tunisia
| | - Rob VAN Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Chedly Chouchani
- Research Laboratory of Environmental Sciences and Technologies, Higher Institute of Environmental Sciences and Technologies of Borj-Cedria, University of Carthage, Hammam-Lif, Tunisia.,Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis El-Manar, Tunisia
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17
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Segers C, Mysara M, Claesen J, Baatout S, Leys N, Lebeer S, Verslegers M, Mastroleo F. Intestinal mucositis precedes dysbiosis in a mouse model for pelvic irradiation. ISME Commun 2021; 1:24. [PMID: 36737646 PMCID: PMC9723693 DOI: 10.1038/s43705-021-00024-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/12/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023]
Abstract
Pelvic radiotherapy is known to evoke intestinal mucositis and dysbiosis. Currently, there are no effective therapies available to mitigate these injuries, which is partly due to a lack of insight into the events causing mucositis and dysbiosis. Here, the complex interplay between the murine host and its microbiome following pelvic irradiation was mapped by characterizing intestinal mucositis along with extensive 16S microbial profiling. We demonstrated important morphological and inflammatory implications within one day after exposure, thereby impairing intestinal functionality and inducing translocation of intraluminal bacteria into mesenteric lymph nodes as innovatively quantified by flow cytometry. Concurrent 16S microbial profiling revealed a delayed impact of pelvic irradiation on beta diversity. Analysis of composition of microbiomes identified biomarkers for pelvic irradiation. Among them, members of the families Ruminococcaceae, Lachnospiraceae and Porphyromonadaceae were differentially affected. Altogether, our unprecedented findings showed how pelvic irradiation evoked structural and functional changes in the intestine, which secondarily resulted in a microbiome shift. Therefore, the presented in vivo irradiation-gut-microbiome platform allows further research into the pathobiology of pelvic irradiation-induced intestinal mucositis and resultant dysbiosis, as well as the exploration of mitigating treatments including drugs and food supplements.
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Affiliation(s)
- Charlotte Segers
- Interdisciplinary Biosciences group, Belgian Nuclear Research Centre SCK CEN, Mol, Belgium
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Mohamed Mysara
- Interdisciplinary Biosciences group, Belgian Nuclear Research Centre SCK CEN, Mol, Belgium
| | - Jürgen Claesen
- Interdisciplinary Biosciences group, Belgian Nuclear Research Centre SCK CEN, Mol, Belgium
- Department of Epidemiology and Data Science, Amsterdam UMC, VU University Amsterdam, Amsterdam, The Netherlands
| | - Sarah Baatout
- Interdisciplinary Biosciences group, Belgian Nuclear Research Centre SCK CEN, Mol, Belgium
- Department of Biotechnology, University of Ghent, Ghent, Belgium
| | - Natalie Leys
- Interdisciplinary Biosciences group, Belgian Nuclear Research Centre SCK CEN, Mol, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Mieke Verslegers
- Interdisciplinary Biosciences group, Belgian Nuclear Research Centre SCK CEN, Mol, Belgium
| | - Felice Mastroleo
- Interdisciplinary Biosciences group, Belgian Nuclear Research Centre SCK CEN, Mol, Belgium.
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18
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van Werkhoven CH, Ducher A, Berkell M, Mysara M, Lammens C, Torre-Cisneros J, Rodríguez-Baño J, Herghea D, Cornely OA, Biehl LM, Bernard L, Dominguez-Luzon MA, Maraki S, Barraud O, Nica M, Jazmati N, Sablier-Gallis F, de Gunzburg J, Mentré F, Malhotra-Kumar S, Bonten MJM, Vehreschild MJGT. Incidence and predictive biomarkers of Clostridioides difficile infection in hospitalized patients receiving broad-spectrum antibiotics. Nat Commun 2021; 12:2240. [PMID: 33854064 PMCID: PMC8046770 DOI: 10.1038/s41467-021-22269-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
Trial enrichment using gut microbiota derived biomarkers by high-risk individuals can improve the feasibility of randomized controlled trials for prevention of Clostridioides difficile infection (CDI). Here, we report in a prospective observational cohort study the incidence of CDI and assess potential clinical characteristics and biomarkers to predict CDI in 1,007 patients ≥ 50 years receiving newly initiated antibiotic treatment with penicillins plus a beta-lactamase inhibitor, 3rd/4th generation cephalosporins, carbapenems, fluoroquinolones or clindamycin from 34 European hospitals. The estimated 90-day cumulative incidences of a first CDI episode is 1.9% (95% CI 1.1-3.0). Carbapenem treatment (Hazard Ratio (95% CI): 5.3 (1.7-16.6)), toxigenic C. difficile rectal carriage (10.3 (3.2-33.1)), high intestinal abundance of Enterococcus spp. relative to Ruminococcus spp. (5.4 (2.1-18.7)), and low Shannon alpha diversity index as determined by 16 S rRNA gene profiling (9.7 (3.2-29.7)), but not normalized urinary 3-indoxyl sulfate levels, predicts an increased CDI risk.
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Affiliation(s)
- Cornelis H van Werkhoven
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | | | - Matilda Berkell
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Mohamed Mysara
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Microbiology Unit, Environment Health and Safety, Belgian Nuclear Research Centre, SCK.CEN, Mol, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Julian Torre-Cisneros
- Maimonides Institute for Research in Biomedicine of Cordoba (IMIBIC), Reina Sofia University Hospital, University of Cordoba (UCO), Cordoba, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain
- Departamento de Medicina, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - Delia Herghea
- Oncology Institute Prof. Dr. I Chiricuta, Cluj Napoca, Romania
| | - Oliver A Cornely
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Chair Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Lena M Biehl
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Louis Bernard
- Centre hospitalo-universitaire de Tours, Tours, France
| | | | - Sofia Maraki
- University Hospital of Heraklion, Heraklion, Greece
| | - Olivier Barraud
- Université Limoges, INSERM U1092, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - Maria Nica
- Infectious and Tropical Diseases Hospital "Dr. Victor Babes", Bucharest, Romania
| | - Nathalie Jazmati
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
- Labor Dr. Wisplinghoff, Cologne, Germany
| | | | | | | | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Maria J G T Vehreschild
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany.
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19
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Berkell M, Mysara M, Xavier BB, van Werkhoven CH, Monsieurs P, Lammens C, Ducher A, Vehreschild MJGT, Goossens H, de Gunzburg J, Bonten MJM, Malhotra-Kumar S. Microbiota-based markers predictive of development of Clostridioides difficile infection. Nat Commun 2021; 12:2241. [PMID: 33854066 PMCID: PMC8047037 DOI: 10.1038/s41467-021-22302-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Antibiotic-induced modulation of the intestinal microbiota can lead to Clostridioides difficile infection (CDI), which is associated with considerable morbidity, mortality, and healthcare-costs globally. Therefore, identification of markers predictive of CDI could substantially contribute to guiding therapy and decreasing the infection burden. Here, we analyze the intestinal microbiota of hospitalized patients at increased CDI risk in a prospective, 90-day cohort-study before and after antibiotic treatment and at diarrhea onset. We show that patients developing CDI already exhibit significantly lower diversity before antibiotic treatment and a distinct microbiota enriched in Enterococcus and depleted of Ruminococcus, Blautia, Prevotella and Bifidobacterium compared to non-CDI patients. We find that antibiotic treatment-induced dysbiosis is class-specific with beta-lactams further increasing enterococcal abundance. Our findings, validated in an independent prospective patient cohort developing CDI, can be exploited to enrich for high-risk patients in prospective clinical trials, and to develop predictive microbiota-based diagnostics for management of patients at risk for CDI.
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Affiliation(s)
- Matilda Berkell
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Mohamed Mysara
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK-CEN, Mol, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Cornelis H van Werkhoven
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Pieter Monsieurs
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK-CEN, Mol, Belgium
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | | | - Maria J G T Vehreschild
- Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | | | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium.
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20
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Rogiers T, Claesen J, Van Gompel A, Vanhoudt N, Mysara M, Williamson A, Leys N, Van Houdt R, Boon N, Mijnendonckx K. Soil microbial community structure and functionality changes in response to long-term metal and radionuclide pollution. Environ Microbiol 2021; 23:1670-1683. [PMID: 33415825 PMCID: PMC8048617 DOI: 10.1111/1462-2920.15394] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 09/11/2020] [Revised: 12/09/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022]
Abstract
Microbial communities are essential for a healthy soil ecosystem. Metals and radionuclides can exert a persistent pressure on the soil microbial community. However, little is known on the effect of long‐term co‐contamination of metals and radionuclides on the microbial community structure and functionality. We investigated the impact of historical discharges of the phosphate and nuclear industry on the microbial community in the Grote Nete river basin in Belgium. Eight locations were sampled along a transect to the river edge and one location further in the field. Chemical analysis demonstrated a metal and radionuclide contamination gradient and revealed a distinct clustering of the locations based on all metadata. Moreover, a relation between the chemical parameters and the bacterial community structure was demonstrated. Although no difference in biomass was observed between locations, cultivation‐dependent experiments showed that communities from contaminated locations survived better on singular metals than communities from control locations. Furthermore, nitrification, a key soil ecosystem process seemed affected in contaminated locations when combining metadata with microbial profiling. These results indicate that long‐term metal and radionuclide pollution impacts the microbial community structure and functionality and provides important fundamental insights into microbial community dynamics in co‐metal‐radionuclide contaminated sites.
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Affiliation(s)
- Tom Rogiers
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium.,Center for Microbial Ecology and Technology (CMET), UGent, Ghent, Belgium
| | - Jürgen Claesen
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Axel Van Gompel
- Biosphere Impact Studies, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Nathalie Vanhoudt
- Biosphere Impact Studies, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Adam Williamson
- Center for Microbial Ecology and Technology (CMET), UGent, Ghent, Belgium
| | - Natalie Leys
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), UGent, Ghent, Belgium
| | - Kristel Mijnendonckx
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
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21
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Laanen P, Saenen E, Mysara M, Van de Walle J, Van Hees M, Nauts R, Van Nieuwerburgh F, Voorspoels S, Jacobs G, Cuypers A, Horemans N. Changes in DNA Methylation in Arabidopsis thaliana Plants Exposed Over Multiple Generations to Gamma Radiation. Front Plant Sci 2021; 12:611783. [PMID: 33868326 PMCID: PMC8044457 DOI: 10.3389/fpls.2021.611783] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/09/2021] [Indexed: 05/05/2023]
Abstract
Previous studies have found indications that exposure to ionising radiation (IR) results in DNA methylation changes in plants. However, this phenomenon is yet to be studied across multiple generations. Furthermore, the exact role of these changes in the IR-induced plant response is still far from understood. Here, we study the effect of gamma radiation on DNA methylation and its effect across generations in young Arabidopsis plants. A multigenerational set-up was used in which three generations (Parent, generation 1, and generation 2) of 7-day old Arabidopsis thaliana plants were exposed to either of the different radiation treatments (30, 60, 110, or 430 mGy/h) or to natural background radiation (control condition) for 14 days. The parental generation consisted of previously non-exposed plants, whereas generation 1 and generation 2 plants had already received a similar irradiation in the previous one or two generations, respectively. Directly after exposure the entire methylomes were analysed with UPLC-MS/MS to measure whole genome methylation levels. Whole genome bisulfite sequencing was used to identify differentially methylated regions (DMRs), including their methylation context in the three generations and this for three different radiation conditions (control, 30 mGy/h, and 110 mGy/h). Both intra- and intergenerational comparisons of the genes and transposable elements associated with the DMRs were made. Taking the methylation context into account, the highest number of changes were found for cytosines followed directly by guanine (CG methylation), whereas only limited changes in CHG methylation occurred and no changes in CHH methylation were observed. A clear increase in IR-induced DMRs was seen over the three generations that were exposed to the lowest dose rate, where generation 2 had a markedly higher number of DMRs than the previous two generations (Parent and generation 1). Counterintuitively, we did not see significant differences in the plants exposed to the highest dose rate. A large number of DMRs associated with transposable elements were found, the majority of them being hypermethylated, likely leading to more genetic stability. Next to that, a significant number of DMRs were associated with genes (either in their promoter-associated region or gene body). A functional analysis of these genes showed an enrichment for genes related to development as well as various stress responses, including DNA repair, RNA splicing, and (a)biotic stress responses. These observations indicate a role of DNA methylation in the regulation of these genes in response to IR exposure and shows a possible role for epigenetics in plant adaptation to IR over multiple generations.
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Affiliation(s)
- Pol Laanen
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium
| | - Eline Saenen
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Mohamed Mysara
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Jorden Van de Walle
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium
| | - May Van Hees
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Robin Nauts
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
- NXTGNT, Ghent University, Ghent, Belgium
| | | | - Griet Jacobs
- Vlaamse Instelling voor Technologisch Onderzoek, VITO, Mol, Belgium
| | - Ann Cuypers
- Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium
| | - Nele Horemans
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Centre for Environmental Research, Hasselt University, Diepenbeek, Belgium
- *Correspondence: Nele Horemans,
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22
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Petit PCM, Pible O, Eesbeeck VV, Alban C, Steinmetz G, Mysara M, Monsieurs P, Armengaud J, Rivasseau C. Direct Meta-Analyses Reveal Unexpected Microbial Life in the Highly Radioactive Water of an Operating Nuclear Reactor Core. Microorganisms 2020; 8:E1857. [PMID: 33255667 PMCID: PMC7760952 DOI: 10.3390/microorganisms8121857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 02/04/2023] Open
Abstract
The pools of nuclear reactor facilities constitute harsh environments for life, bathed with ionizing radiation, filled with demineralized water and containing toxic radioactive elements. The very few studies published to date have explored water pools used to store spent nuclear fuels. Due to access restrictions and strong handling constraints related to the high radioactivity level, nothing is presently known about life in water pools that directly cool nuclear cores. In this work, we investigated the microbial communities in the cooling pool of the French Osiris nuclear reactor using direct meta-omics approaches, namely, DNA metabarcoding and proteotyping based on 16S ribosomal RNA gene sequencing and on peptide analysis, respectively. We identified 25 genera in the highly radioactive core water supply during operation with radionuclide activity higher than 3 × 109 Bq/m3. The prevailing genera Variovorax and Sphingomonas at operation were supplanted by Methylobacterium, Asanoa, and Streptomyces during shutdown. Variovorax might use dihydrogen produced by water radiolysis as an energy source.
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Affiliation(s)
- Pauline C. M. Petit
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), CNRS, INRAE, Université Grenoble Alpes, F-38054 Grenoble, France; (P.C.M.P.); (C.A.)
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, F-30200 Bagnols-sur-Cèze, France; (O.P.); (G.S.); (J.A.)
| | - Valérie Van Eesbeeck
- Microbiology Unit, The Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium; (V.V.E.); (M.M.); (P.M.)
| | - Claude Alban
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), CNRS, INRAE, Université Grenoble Alpes, F-38054 Grenoble, France; (P.C.M.P.); (C.A.)
| | - Gérard Steinmetz
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, F-30200 Bagnols-sur-Cèze, France; (O.P.); (G.S.); (J.A.)
| | - Mohamed Mysara
- Microbiology Unit, The Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium; (V.V.E.); (M.M.); (P.M.)
| | - Pieter Monsieurs
- Microbiology Unit, The Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium; (V.V.E.); (M.M.); (P.M.)
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris-Saclay, F-30200 Bagnols-sur-Cèze, France; (O.P.); (G.S.); (J.A.)
| | - Corinne Rivasseau
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), CNRS, INRAE, Université Grenoble Alpes, F-38054 Grenoble, France; (P.C.M.P.); (C.A.)
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23
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Goussarov G, Cleenwerck I, Mysara M, Leys N, Monsieurs P, Tahon G, Carlier A, Vandamme P, Van Houdt R. PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing. Bioinformatics 2020; 36:2337-2344. [PMID: 31899493 PMCID: PMC7178395 DOI: 10.1093/bioinformatics/btz964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/21/2019] [Accepted: 12/30/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a novel method based on short-oligonucleotide frequencies to compute inter-genomic distances. RESULTS Our tetranucleotide and hexanucleotide implementations, which were optimized based on a taxonomically well-defined set of over 200 newly sequenced bacterial genomes, are as accurate as the short oligonucleotide-based method TETRA and average nucleotide identity, for identifying bacterial species and strains, respectively. Moreover, the lightweight nature of this method makes it applicable for large-scale analyses. AVAILABILITY AND IMPLEMENTATION The method introduced here was implemented, together with other existing methods, in a dependency-free software written in C, GenDisCal, available as source code from https://github.com/LM-UGent/GenDisCal. The software supports multithreading and has been tested on Windows and Linux (CentOS). In addition, a Java-based graphical user interface that acts as a wrapper for the software is also available. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gleb Goussarov
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Ilse Cleenwerck
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Pieter Monsieurs
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
| | - Guillaume Tahon
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Aurélien Carlier
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Peter Vandamme
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
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Fahrion J, Fink C, Zabel P, Schubert D, Mysara M, Van Houdt R, Eikmanns B, Beblo-Vranesevic K, Rettberg P. Microbial Monitoring in the EDEN ISS Greenhouse, a Mobile Test Facility in Antarctica. Front Microbiol 2020; 11:525. [PMID: 32296408 PMCID: PMC7137377 DOI: 10.3389/fmicb.2020.00525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/11/2020] [Indexed: 11/13/2022] Open
Abstract
The EDEN ISS greenhouse, integrated in two joined containers, is a confined mobile test facility in Antarctica for the development and optimization of new plant cultivation techniques for future space programs. The EDEN ISS greenhouse was used successfully from February to November 2018 for fresh food production for the overwintering crew at the Antarctic Neumayer III station. During the 9 months of operation, samples from the different plants, from the nutrition solution of the aeroponic planting system, and from diverse surfaces within the three different compartments of the container were taken [future exploration greenhouse (FEG), service section (SS), and cold porch (CP)]. Quantity as well as diversity of microorganisms was examined by cultivation. In case of the plant samples, microbial quantities were in a range from 102 to 104 colony forming units per gram plant material. Compared to plants purchased from a German grocery, the produce hosted orders of magnitude more microorganisms than the EDEN ISS plants. The EDEN ISS plant samples contained mainly fungi and a few bacteria. No classical food associated pathogenic microorganism, like Escherichia and Salmonella, could be found. Probably due to the used cultivation approach, Archaea were not found in the samples. The bioburden in the nutrition solutions increased constantly over time but never reached critical values like 102-103 cfu per 100 mL in irrigation water as it is stated, e.g., for commercial European plant productions. The surface samples revealed high differences in the microbial burden between the greenhouse part of the container and the SS and CP part. However, the numbers of organisms (bacteria and fungi) found in the planted greenhouse were still not critical. The microbial loaded surfaces showed strong temporal as well as spatial fluctuations. In samples of the nutrition solution and the surface, the amount of bacteria exceeded the amount of fungi by many times. For identification, 16S rRNA gene sequencing was performed for the isolated prokaryotic organisms. Phylogenetic analyses revealed that the most abundant bacterial phyla were Firmicutes and Actinobacteria. These phyla include plant- and human-associated bacterial species. In general, it could be shown that it is possible to produce edible fresh food in a remote environment and this food is safe for consumption from a microbiological point of view.
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Affiliation(s)
- Jana Fahrion
- Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute of Microbiology and Biotechnology, Faculty of Natural Sciences, University of Ulm, Ulm, Germany
| | - Carina Fink
- Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Paul Zabel
- Institute for Space Systems, German Aerospace Center (DLR), Bremen, Germany
| | - Daniel Schubert
- Institute for Space Systems, German Aerospace Center (DLR), Bremen, Germany
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Bernhard Eikmanns
- Institute of Microbiology and Biotechnology, Faculty of Natural Sciences, University of Ulm, Ulm, Germany
| | | | - Petra Rettberg
- Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
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Robles-Aguilar AA, Grunert O, Hernandez-Sanabria E, Mysara M, Meers E, Boon N, Jablonowski ND. Effect of Applying Struvite and Organic N as Recovered Fertilizers on the Rhizosphere Dynamics and Cultivation of Lupine ( Lupinus angustifolius). Front Plant Sci 2020; 11:572741. [PMID: 33329631 PMCID: PMC7717983 DOI: 10.3389/fpls.2020.572741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/19/2020] [Indexed: 05/11/2023]
Abstract
Intensive agriculture and horticulture heavily rely on the input of fertilizers to sustain food (and feed) production. However, high carbon footprint and pollution are associated with the mining processes of P and K, and the artificial nitrogen fixation for the production of synthetic fertilizers. Organic fertilizers or recovered nutrients from different waste sources can be used to reduce the environmental impact of fertilizers. We tested two recovered nutrients with slow-release patterns as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as a nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in lupine plants. Plant performance was not affected by the fertilizer applied; however, N recovery was higher from the organic fertilizer than from struvite. As root architecture is fundamental for plant productivity, variations in root structure and length as a result of soil nutrient availability driven by plant-bacteria interactions were compared showing also no differences between fertilizers. However, fertilized plants were considerably different in the root length and morphology compared with the no fertilized plants. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed that the fertilizer applied had a significant impact on the associations and functionality of the bacteria inhabiting the growing medium used. The type of fertilizer significantly influenced the interindividual dissimilarities in the most abundant genera between treatments. This means that different plant species have a distinct effect on modulating the associated microbial community, but in the case of lupine, the fertilizer had a bigger effect than the plant itself. These novel insights on interactions between recovered fertilizers, plant, and associated microbes can contribute to developing sustainable crop production systems.
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Affiliation(s)
- Ana A. Robles-Aguilar
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Jülich, Germany
| | - Oliver Grunert
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
- Greenyard Horticulture, Ghent, Belgium
| | - Emma Hernandez-Sanabria
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Bacteriology, VIB – KU Leuven Center for Microbiology, Rega Institute, Leuven, Belgium
| | - Mohamed Mysara
- Unit of Microbiology, Belgian Nuclear Research Center, StudieCentrum voor Kernenergie⋅Centre d’étude de l’Energie Nucléaire (SCK⋅CEN), Mol, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Erik Meers
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
- *Correspondence: Nico Boon,
| | - Nicolai D. Jablonowski
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Jülich, Germany
- Nicolai D. Jablonowski,
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Xavier BB, Mysara M, Bolzan M, Ribeiro-Gonçalves B, Alako BTF, Harrison P, Lammens C, Kumar-Singh S, Goossens H, Carriço JA, Cochrane G, Malhotra-Kumar S. BacPipe: A Rapid, User-Friendly Whole-Genome Sequencing Pipeline for Clinical Diagnostic Bacteriology. iScience 2019; 23:100769. [PMID: 31887656 PMCID: PMC6941874 DOI: 10.1016/j.isci.2019.100769] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/21/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023] Open
Abstract
Despite rapid advances in whole genome sequencing (WGS) technologies, their integration into routine microbiological diagnostics has been hampered by the lack of standardized downstream bioinformatics analysis. We developed a comprehensive and computationally low-resource bioinformatics pipeline (BacPipe) enabling direct analyses of bacterial whole-genome sequences (raw reads or contigs) obtained from second- or third-generation sequencing technologies. A graphical user interface was developed to visualize real-time progression of the analysis. The scalability and speed of BacPipe in handling large datasets was demonstrated using 4,139 Illumina paired-end sequence files of publicly available bacterial genomes (2.9–5.4 Mb) from the European Nucleotide Archive. BacPipe is integrated in EBI-SELECTA, a project-specific portal (H2020-COMPARE), and is available as an independent docker image that can be used across Windows- and Unix-based systems. BacPipe offers a fully automated “one-stop” bacterial WGS analysis pipeline to overcome the major hurdle of WGS data analysis in hospitals and public-health and for infection control monitoring. BacPipe is an automated whole genome sequencing pipeline Interactive user-friendly GUI BacPipe can process raw reads, contigs, or scaffolds Time-to-analysis for a 5 Mb genome is ∼30–40 min
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Affiliation(s)
- Basil B Xavier
- Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium
| | - Mohamed Mysara
- Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium; Microbiology Unit, Belgian Nuclear Research Center (SCK•CEN), Mol 2400, Belgium
| | - Mattia Bolzan
- Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Bruno Ribeiro-Gonçalves
- Instituto de Microbiologia and Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, Lisboa 1649-028, Portugal
| | - Blaise T F Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Peter Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Christine Lammens
- Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium
| | - Samir Kumar-Singh
- Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Molecular Pathology Group, Cell Biology and Histology, University of Antwerp, Antwerp 2610, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium
| | - João A Carriço
- Instituto de Microbiologia and Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, Lisboa 1649-028, Portugal
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Campus Drie Eiken, University of Antwerp, S6, Universiteitsplein 1, B-2610 Wilrijk, Belgium; Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp 2610, Belgium.
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Grunert O, Robles-Aguilar AA, Hernandez-Sanabria E, Schrey SD, Reheul D, Van Labeke MC, Vlaeminck SE, Vandekerckhove TGL, Mysara M, Monsieurs P, Temperton VM, Boon N, Jablonowski ND. Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media. Sci Rep 2019; 9:9561. [PMID: 31266970 PMCID: PMC6606572 DOI: 10.1038/s41598-019-45290-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/04/2019] [Indexed: 11/09/2022] Open
Abstract
Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.
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Affiliation(s)
- Oliver Grunert
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium.,Greenyard, Skaldenstraat 7a, 9042, Desteldonk, Belgium
| | - Ana A Robles-Aguilar
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, 52428, Jülich, Germany.,Laboratory of Analytical Chemistry and Applied Ecochemistry, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Emma Hernandez-Sanabria
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Silvia D Schrey
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, 52428, Jülich, Germany
| | - Dirk Reheul
- Department of Plant and Crops, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | | | - Siegfried E Vlaeminck
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium.,Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - Tom G L Vandekerckhove
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Mohamed Mysara
- Unit of Microbiology, Belgian Nuclear Research Center (SCK•CEN), Mol, Belgium.,Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Pieter Monsieurs
- Unit of Microbiology, Belgian Nuclear Research Center (SCK•CEN), Mol, Belgium.,Unit Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Vicky M Temperton
- Institute of Ecology, Leuphana University Lüneburg, Universitätsallee 1, D-21335, Lüneburg, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Gent, Belgium.
| | - Nicolai D Jablonowski
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, 52428, Jülich, Germany.
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Ramadan R, Vromans E, Anang DC, Decrock E, Mysara M, Monsieurs P, Baatout S, Leybaert L, Aerts A. Single and fractionated ionizing radiation induce alterations in endothelial connexin expression and channel function. Sci Rep 2019; 9:4643. [PMID: 31217426 PMCID: PMC6584668 DOI: 10.1038/s41598-019-39317-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 08/30/2018] [Accepted: 12/14/2018] [Indexed: 12/11/2022] Open
Abstract
Radiotherapy is an effective treatment for most tumor types. However, emerging evidence indicates an increased risk for atherosclerosis after ionizing radiation exposure, initiated by endothelial cell dysfunction. Interestingly, endothelial cells express connexin (Cx) proteins that are reported to exert proatherogenic as well as atheroprotective effects. Furthermore, Cxs form channels, gap junctions and hemichannels, that are involved in bystander signaling that leads to indirect radiation effects in non-exposed cells. We here aimed to investigate the consequences of endothelial cell irradiation on Cx expression and channel function. Telomerase immortalized human Coronary Artery/Microvascular Endothelial cells were exposed to single and fractionated X-rays. Several biological endpoints were investigated at different time points after exposure: Cx gene and protein expression, gap junctional dye coupling and hemichannel function. We demonstrate that single and fractionated irradiation induce upregulation of proatherogenic Cx43 and downregulation of atheroprotective Cx40 gene and protein levels in a dose-dependent manner. Single and fractionated irradiation furthermore increased gap junctional communication and induced hemichannel opening. Our findings indicate alterations in Cx expression that are typically observed in endothelial cells covering atherosclerotic plaques. The observed radiation-induced increase in Cx channel function may promote bystander signaling thereby exacerbating endothelial cell damage and atherogenesis.
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Affiliation(s)
- Raghda Ramadan
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
- Department of Basic and Applied Medical Sciences, Physiology group, Ghent University, Ghent, Belgium
| | - Els Vromans
- Centre for Environmental Health Sciences, Hasselt University, Hasselt, Belgium
| | - Dornatien Chuo Anang
- Biomedical Research Institute and transnational university of Limburg, Hasselt University, Hasselt, Belgium
| | - Elke Decrock
- Department of Basic and Applied Medical Sciences, Physiology group, Ghent University, Ghent, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - Pieter Monsieurs
- Microbiology Unit, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium
- Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Luc Leybaert
- Department of Basic and Applied Medical Sciences, Physiology group, Ghent University, Ghent, Belgium
| | - An Aerts
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK·CEN), Mol, Belgium.
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Byloos B, Monsieurs P, Mysara M, Leys N, Boon N, Van Houdt R. Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages. BMC Microbiol 2018; 18:122. [PMID: 30249184 PMCID: PMC6154810 DOI: 10.1186/s12866-018-1262-0] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/17/2018] [Indexed: 11/25/2022] Open
Abstract
Background Basalt is the most common igneous rock on the Earth’s surface covering. Basalt-associated microorganisms drive the cycling and sequestration of different elements such as nitrogen, carbon and other nutrients, which facilitate subsequent pioneer and plant development, impacting long-term regulation of the Earth’s temperature and biosphere. The initial processes of colonization and subsequent rock weathering by microbial communities are still poorly understood and relatively few data are available on the diversity and richness of the communities inhabiting successive and chronological lava flows. In this study, the bacterial communities present on lava deposits from different eruptions of the 1975–84 Krafla Fires (32-, 35- and 39-year old, respectively) at the Krafla, Iceland, were determined. Results Three sites were sampled for each deposit (32-, 35- and 39-year old), two proximal sites (at 10 m distance) and one more distant site (at 100 m from the two other sites). The determined chemical composition and metal concentrations were similar for the three basalt deposits. No significant differences were observed in the total number of cells in each flow. 16S rRNA gene amplicon sequencing showed that the most abundant classified phylum across the 3 flows was Proteobacteria, although predominance of Acidobacteria, Actinobacteria and Firmicutes was observed for some sampling sites. In addition, a considerable fraction of the operational taxonomic units remained unclassified. Alpha diversity (Shannon, inverse Simpson and Chao), HOMOVA and AMOVA only showed a significant difference for Shannon between the 32- and 39-year old flow (p < 0.05). Nonmetric multidimensional scaling (NMDS) analysis showed that age significantly (p = 0.026) influenced the leftward movement along NMDS axis 1. Conclusions Although NMDS indicated that the (relatively small) age difference of the deposits appeared to impact the bacterial community, this analysis was not consistent with AMOVA and HOMOVA, indicating no significant difference in community structure. The combined results drive us to conclude that the (relatively small) age differences of the deposits do not appear to be the main factor shaping the microbial communities. Probably other factors such as spatial heterogeneity, associated carbon content, exogenous rain precipitations and wind also affect the diversity and dynamics. Electronic supplementary material The online version of this article (10.1186/s12866-018-1262-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bo Byloos
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, Boeretang 200, B-2400, Mol, Belgium.,Center for Microbial Ecology & Technology (CMET), Ghent University, Ghent, Belgium
| | - Pieter Monsieurs
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, Boeretang 200, B-2400, Mol, Belgium
| | - Mohamed Mysara
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, Boeretang 200, B-2400, Mol, Belgium
| | - Natalie Leys
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, Boeretang 200, B-2400, Mol, Belgium
| | - Nico Boon
- Center for Microbial Ecology & Technology (CMET), Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, Boeretang 200, B-2400, Mol, Belgium.
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30
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Macaeva E, Mysara M, De Vos WH, Baatout S, Quintens R. Gene expression-based biodosimetry for radiological incidents: assessment of dose and time after radiation exposure. Int J Radiat Biol 2018; 95:64-75. [PMID: 30247087 DOI: 10.1080/09553002.2018.1511926] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 10/28/2022]
Abstract
PURPOSE In order to ensure efficient use of medical resources following a radiological incident, there is an urgent need for high-throughput time-efficient biodosimetry tools. In the present study, we tested the applicability of a gene expression signature for the prediction of exposure dose as well as the time elapsed since irradiation. MATERIALS AND METHODS We used whole blood samples from seven healthy volunteers as reference samples (X-ray doses: 0, 25, 50, 100, 500, 1000, and 2000 mGy; time points: 8, 12, 24, 36 and 48 h) and samples from seven other individuals as 'blind samples' (20 samples in total). RESULTS Gene expression values normalized to the reference gene without normalization to the unexposed controls were sufficient to predict doses with a correlation coefficient between the true and the predicted doses of 0.86. Importantly, we could also classify the samples according to the time since exposure with a correlation coefficient between the true and the predicted time point of 0.96. Because of the dynamic nature of radiation-induced gene expression, this feature will be of critical importance for adequate gene expression-based dose prediction in a real emergency situation. In addition, in this study we also compared different methodologies for RNA extraction available on the market and suggested the one most suitable for emergency situation which does not require on-spot availability of any specific reagents or equipment. CONCLUSIONS Our results represent an important advancement in the application of gene expression for biodosimetry purposes.
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Affiliation(s)
- Ellina Macaeva
- a Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK•CEN, Mol , Belgium.,b Department of Molecular Biotechnology , Ghent University , Ghent , Belgium
| | - Mohamed Mysara
- a Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK•CEN, Mol , Belgium
| | - Winnok H De Vos
- b Department of Molecular Biotechnology , Ghent University , Ghent , Belgium.,c Department of Veterinary Sciences , University of Antwerp , Belgium
| | - Sarah Baatout
- a Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK•CEN, Mol , Belgium.,b Department of Molecular Biotechnology , Ghent University , Ghent , Belgium
| | - Roel Quintens
- a Interdisciplinary Biosciences Group, Belgian Nuclear Research Centre, SCK•CEN, Mol , Belgium
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Mysara M, Njima M, Leys N, Raes J, Monsieurs P. From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data. Gigascience 2017; 6:1-10. [PMID: 28369460 PMCID: PMC5466709 DOI: 10.1093/gigascience/giw017] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/27/2016] [Indexed: 01/09/2023] Open
Abstract
The development of high-throughput sequencing technologies has provided microbial ecologists with an efficient approach to assess bacterial diversity at an unseen depth, particularly with the recent advances in the Illumina MiSeq sequencing platform. However, analyzing such high-throughput data is posing important computational challenges, requiring specialized bioinformatics solutions at different stages during the processing pipeline, such as assembly of paired-end reads, chimera removal, correction of sequencing errors, and clustering of those sequences into Operational Taxonomic Units (OTUs). Individual algorithms grappling with each of those challenges have been combined into various bioinformatics pipelines, such as mothur, QIIME, LotuS, and USEARCH. Using a set of well-described bacterial mock communities, state-of-the-art pipelines for Illumina MiSeq amplicon sequencing data are benchmarked at the level of the amount of sequences retained, computational cost, error rate, and quality of the OTUs. In addition, a new pipeline called OCToPUS is introduced, which is making an optimal combination of different algorithms. Huge variability is observed between the different pipelines in respect to the monitored performance parameters, where in general the amount of retained reads is found to be inversely proportional to the quality of the reads. By contrast, OCToPUS achieves the lowest error rate, minimum number of spurious OTUs, and the closest correspondence to the existing community, while retaining the uppermost amount of reads when compared to other pipelines. The newly introduced pipeline translates Illumina MiSeq amplicon sequencing data into high-quality and reliable OTUs, with improved performance and accuracy compared to the currently existing pipelines.
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Affiliation(s)
- Mohamed Mysara
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400 Mol, Belgium.,Department of Bio-Engineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium.,VIB Center for the Biology of Disease, VIB, Herestraat 49 - box 1028, 3000 Leuven, Belgium.,Department of Microbiology and Immunology, REGA institute, Herestraat 49 - box 1028, 3000 Leuven, Belgium
| | - Mercy Njima
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400 Mol, Belgium
| | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400 Mol, Belgium
| | - Jeroen Raes
- Department of Bio-Engineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium.,VIB Center for the Biology of Disease, VIB, Herestraat 49 - box 1028, 3000 Leuven, Belgium.,Department of Microbiology and Immunology, REGA institute, Herestraat 49 - box 1028, 3000 Leuven, Belgium
| | - Pieter Monsieurs
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400 Mol, Belgium
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Mysara M, Vandamme P, Props R, Kerckhof FM, Leys N, Boon N, Raes J, Monsieurs P. Reconciliation between operational taxonomic units and species boundaries. FEMS Microbiol Ecol 2017; 93:3065615. [PMID: 28334218 PMCID: PMC5812548 DOI: 10.1093/femsec/fix029] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [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: 07/01/2016] [Accepted: 03/09/2017] [Indexed: 01/20/2023] Open
Abstract
The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into operational taxonomic units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for bacterial species. Our results show that the robustness of such a generalised cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene. It will lead to biases in diversity metrics and makes it hard to compare results obtained with amplicons derived with different primer sets. The method introduced within this work takes into account the differential evolutional rates of taxonomic lineages in order to define a dynamic and taxonomic-dependent OTU clustering cut-off score. For a taxonomic family consisting of species showing high evolutionary conservation in the amplified variable regions, the cut-off will be more stringent than 97%. By taking into consideration the amplified variable regions and the taxonomic family when defining this cut-off, such a threshold will lead to more robust results and closer correspondence between OTUs and species. This approach has been implemented in a publicly available software package called DynamiC.
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Affiliation(s)
- Mohamed Mysara
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), 2400 Mol, Belgium.,Department of Bio-Engineering sciences, Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium.,VIB lab for Bioinformatics and (eco-)systems biology, VIB, 3000 Leuven, Belgium.,Department of Microbiology and Immunology, REGA institute, KU Leuven, 3000 Leuven, Belgium
| | - Peter Vandamme
- Department of Biochemistry and microbiology, Ghent University, 9000 Ghent, Belgium
| | - Ruben Props
- Department of Biochemical and microbial technology, Ghent University, 9000 Ghent, Belgium
| | | | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), 2400 Mol, Belgium
| | - Nico Boon
- Department of Biochemical and microbial technology, Ghent University, 9000 Ghent, Belgium
| | - Jeroen Raes
- VIB lab for Bioinformatics and (eco-)systems biology, VIB, 3000 Leuven, Belgium.,Department of Microbiology and Immunology, REGA institute, KU Leuven, 3000 Leuven, Belgium
| | - Pieter Monsieurs
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), 2400 Mol, Belgium
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Affiliation(s)
- Ruben Props
- Center for Microbial Ecology and Technology (CMET) Ghent University Coupure Links 653 B‐9000 Gent Belgium
- Belgian Nuclear Research Centre (SCK•CEN) Boeretang 200 B‐2400 Mol Belgium
| | - Pieter Monsieurs
- Belgian Nuclear Research Centre (SCK•CEN) Boeretang 200 B‐2400 Mol Belgium
| | - Mohamed Mysara
- Belgian Nuclear Research Centre (SCK•CEN) Boeretang 200 B‐2400 Mol Belgium
| | - Lieven Clement
- Department of Applied Mathematics, Informatics and Statistics Ghent University B‐9000 Gent Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET) Ghent University Coupure Links 653 B‐9000 Gent Belgium
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Mysara M, Leys N, Raes J, Monsieurs P. IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data. BMC Bioinformatics 2016; 17:192. [PMID: 27130479 PMCID: PMC4850673 DOI: 10.1186/s12859-016-1061-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 04/21/2016] [Indexed: 08/26/2023] Open
Abstract
Background The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S rRNA gene amplicon sequencing). Denoising, the removal of sequencing errors, is an important step in preprocessing amplicon sequencing data. The increasing popularity of the Illumina MiSeq platform for these applications requires the development of appropriate denoising methods. Results The newly proposed denoising algorithm IPED includes a machine learning method which predicts potentially erroneous positions in sequencing reads based on a combination of quality metrics. Subsequently, this information is used to group those error-containing reads with correct reads, resulting in error-free consensus reads. This is achieved by masking potentially erroneous positions during this clustering step. Compared to the second best algorithm available, IPED detects double the amount of errors. Reducing the error rate had a positive effect on the clustering of reads in operational taxonomic units, with an almost perfect correspondence between the number of clusters and the theoretical number of species present in the mock communities. Conclusion Our algorithm IPED is a powerful denoising tool for correcting sequencing errors in Illumina MiSeq 16S rRNA gene amplicon sequencing data. Apart from significantly reducing the error rate of the sequencing reads, it has also a beneficial effect on their clustering into operational taxonomic units. IPED is freely available at http://science.sckcen.be/en/Institutes/EHS/MCB/MIC/Bioinformatics/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1061-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohamed Mysara
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Mol, Belgium.,Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium.,VIB Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, REGA institute, KU Leuven, Belgium
| | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Mol, Belgium
| | - Jeroen Raes
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, REGA institute, KU Leuven, Belgium
| | - Pieter Monsieurs
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Mol, Belgium.
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Mysara M, Leys N, Raes J, Monsieurs P. NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads. BMC Bioinformatics 2015; 16:88. [PMID: 25888405 PMCID: PMC4403973 DOI: 10.1186/s12859-015-0520-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/26/2015] [Indexed: 11/10/2022] Open
Abstract
Background The popularity of new sequencing technologies has led to an explosion of possible applications, including new approaches in biodiversity studies. However each of these sequencing technologies suffers from sequencing errors originating from different factors. For 16S rRNA metagenomics studies, the 454 pyrosequencing technology is one of the most frequently used platforms, but sequencing errors still lead to important data analysis issues (e.g. in clustering in taxonomic units and biodiversity estimation). Moreover, retaining a higher portion of the sequencing data by preserving as much of the read length as possible while maintaining the error rate within an acceptable range, will have important consequences at the level of taxonomic precision. Results The new error correction algorithm proposed in this work - NoDe (Noise Detector) - is trained to identify those positions in 454 sequencing reads that are likely to have an error, and subsequently clusters those error-prone reads with correct reads resulting in error-free representative read. A benchmarking study with other denoising algorithms shows that NoDe can detect up to 75% more errors in a large scale mock community dataset, and this with a low computational cost compared to the second best algorithm considered in this study. The positive effect of NoDe in 16S rRNA studies was confirmed by the beneficial effect on the precision of the clustering of pyrosequencing reads in operational taxonomic units. Conclusions NoDe was shown to be a computational efficient denoising algorithm for pyrosequencing reads, producing the lowest error rates in an extensive benchmarking study with other denoising algorithms. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0520-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohamed Mysara
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium. .,Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium. .,VIB Center for the Biology of Disease, VIB, Leuven, Belgium.
| | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.
| | - Jeroen Raes
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium. .,VIB Center for the Biology of Disease, VIB, Leuven, Belgium. .,Department of Microbiology and Immunology, REGA institute, KU, Leuven, Belgium.
| | - Pieter Monsieurs
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.
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Mysara M, Elhefnawi M, Garibaldi JM. MysiRNA: Improving siRNA efficacy prediction using a machine-learning model combining multi-tools and whole stacking energy (ΔG). J Biomed Inform 2012; 45:528-34. [DOI: 10.1016/j.jbi.2012.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 01/25/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
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