1
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Dungan AM, Geissler L, Williams AS, Gotze CR, Flynn EC, Blackall LL, van Oppen MJH. DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta. ENVIRONMENTAL MICROBIOME 2023; 18:86. [PMID: 38062479 PMCID: PMC10704692 DOI: 10.1186/s40793-023-00541-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/23/2023] [Indexed: 06/30/2024]
Abstract
BACKGROUND Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages. RESULTS By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A. loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, > 30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A. loripes and P. acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity. CONCLUSIONS Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.
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Affiliation(s)
- Ashley M Dungan
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia.
| | - Laura Geissler
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda S Williams
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Cecilie Ravn Gotze
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Emily C Flynn
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Linda L Blackall
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Madeleine J H van Oppen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
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2
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Browett LC, Ruiz-Lopez S, Mossman HL, Dean AP, Rivett DW. Prior exposure of microbial communities to seawater reduces resilience but increases compositional and functional resistance to flooding events. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165040. [PMID: 37385495 DOI: 10.1016/j.scitotenv.2023.165040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023]
Abstract
Storm surges, flooding, and the encroachment of seawater onto agricultural land are predicted to increase with climate change. These flooding events fundamentally alter many soil properties and have knock-on effects on the microbial community composition and its functioning. The hypotheses tested in this study were (1) that the extent of change (resistance) of microbial community functioning and structure during seawater flooding is a factor of pre-adaptation to the stress, and (2) if structure and function are altered, the pre-adaptation will result in communities returning to previous state prior to flooding (resilience) faster than unexposed communities. We chose a naturally occurring saltmarsh-terrestrial pasture gradient from which three elevations were selected to create mesocosms. By selecting these sites, we were able to incorporate the legacy of differing levels of seawater ingress and exposure. Mesocosms were submerged in seawater for 0, 1, 96- and 192-h, with half of the mesocosms sacrificed immediately after flooding, and the other half taken after a 14 day "recovery" period. The following parameters were monitored: 1) changes in soil environmental parameters, 2) prokaryotic community composition, and 3) microbial functioning. Our results indicated that any length of seawater inundation significantly altered the physicochemical properties of all the soils, although a greater change is observed in the pasture site compared to the saltmarsh sites. These changes remained following a recovery period. Interestingly, our results indicated that for community composition, there was a high degree of resistance for the Saltmarsh mesocosms, with the Pasture mesocosm displaying higher resilience. Further, we observed a functional shift in the enzyme activities with labile hemicellulose being preferentially utilised over cellulose, with the effect increasing with longer floods. These results suggest that changing bacterial physiology is more critical to understanding the impact of storm surges on agricultural systems than bulk community change.
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Affiliation(s)
- Lewis C Browett
- Ecology and the Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Sharon Ruiz-Lopez
- Ecology and the Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Hannah L Mossman
- Ecology and the Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Andrew P Dean
- Ecology and the Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK..
| | - Damian W Rivett
- Ecology and the Environment Research Centre, Department of Natural Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK..
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3
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Hatfield L, Bianco B, Gavillet H, Burns P, Rivett D, Smith M, Jones A, van der Gast C, Horsley A. Effects of postage on recovery of pathogens from cystic fibrosis sputum samples. J Cyst Fibros 2023; 22:816-822. [PMID: 36934050 DOI: 10.1016/j.jcf.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Regular surveillance microbiology of sputum is used in cystic fibrosis (CF) to monitor for new pathogens and target treatments. A move to remote clinics has meant greater reliance on samples collected at home and posted back. The impact of delays and sample disruption caused by posting has not been systematically assessed but could have significant implications for CF microbiology. METHODS Sputum samples collected from adult CF patients were mixed, split, and either processed immediately or posted back to laboratory. Processing involved a further split into aliquots for culture-dependant and-independent microbiology (quantitative PCR [QPCR] and microbiota sequencing). We calculated retrieval by both approaches for five typical CF pathogens: Pseudomonas aeruginosa, Burkholderia cepacia complex, Achromobacter xylosoxidans, Staphylococcus aureus and Stenotrophomonas maltophilia. RESULTS 93 paired samples were collected from 73 CF patients. Median interval between sample posting and receipt was 5 days (range 1-10). For culture, overall concordance for posted and fresh samples was 86% across the five targeted pathogens (ranging from 57 to 100% for different organisms), with no bias towards either sample type. For QPCR, overall concordance was 62% (range 39-84%), again with no bias towards fresh or posted samples. There were no significant differences in culture or QPCR for samples with short (≤3days) versus extended (≥7days) postal delays. Posting had no significant impact on pathogen abundance nor on microbiota characteristics. CONCLUSIONS Posted sputum samples reliably reproduced culture-based and molecular microbiology of freshly collected samples, even after prolonged delays at ambient conditions. This supports use of posted samples during remote monitoring.
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Affiliation(s)
- Lauren Hatfield
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Brooke Bianco
- Manchester Adult Cystic Fibrosis Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Helen Gavillet
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Phillipa Burns
- Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull Royal Infirmary, Hull, United Kingdom
| | - Damian Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Matthew Smith
- UK Health Security Agency, Manchester, United Kingdom; Manchester Medical Microbiology Partnership, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Andrew Jones
- Manchester Adult Cystic Fibrosis Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Christopher van der Gast
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom; Department of Respiratory Medicine, Northern Care Alliance NHS Foundation Trust, Salford, United Kingdom.
| | - Alexander Horsley
- Manchester Adult Cystic Fibrosis Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, United Kingdom.
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4
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Marsh R, Dos Santos C, Hanson L, Ng C, Major G, Smyth AR, Rivett D, van der Gast C. Tezacaftor/Ivacaftor therapy has negligible effects on the cystic fibrosis gut microbiome. Microbiol Spectr 2023; 11:e0117523. [PMID: 37607068 PMCID: PMC10581179 DOI: 10.1128/spectrum.01175-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/28/2023] [Indexed: 08/24/2023] Open
Abstract
People with cystic fibrosis (pwCF) experience a range of persistent gastrointestinal symptoms throughout life. There is evidence indicating interaction between the microbiota and gut pathophysiology in CF. However, there is a paucity of knowledge on the potential effects of CF transmembrane conductance regulator (CFTR) modulator therapies on the gut microbiome. In a pilot study, we investigated the impact of Tezacaftor/Ivacaftor dual combination CFTR modulator therapy on the gut microbiota and metabolomic functioning in pwCF. Fecal samples from 12 pwCF taken at baseline and following placebo or Tezacaftor/Ivacaftor administration were subjected to microbiota sequencing and to targeted metabolomics to assess the short-chain fatty acid (SCFA) composition. Ten healthy matched controls were included as a comparison. Inflammatory calprotectin levels and patient symptoms were also investigated. No significant differences were observed in overall gut microbiota characteristics between any of the study stages, extended also across intestinal inflammation, gut symptoms, and SCFA-targeted metabolomics. However, microbiota and SCFA metabolomic compositions, in pwCF, were significantly different from controls in all study treatment stages. CFTR modulator therapy with Tezacaftor/Ivacaftor had negligible effects on both the gut microbiota and SCFA composition across the course of the study and did not alter toward compositions observed in healthy controls. Future longitudinal CFTR modulator studies will investigate more effective CFTR modulators and should use prolonged sampling periods, to determine whether longer-term changes occur in the CF gut microbiome. IMPORTANCE People with cystic fibrosis (pwCF) experience persistent gastrointestinal (GI) symptoms throughout life. The research question "how can we relieve gastrointestinal symptoms, such as stomach pain, bloating, and nausea?" remains a top priority for clinical research in CF. While CF transmembrane conductance regulator (CFTR) modulator therapies are understood to correct underlying issues of CF disease and increasing the numbers of pwCF are now receiving some form of CFTR modulator treatment. It is not known how these therapies affect the gut microbiome or GI system. In this pilot study, we investigated, for the first time, effects of the dual combination CFTR modulator medicine, Tezacaftor/Ivacaftor. We found it had negligible effects on patient GI symptoms, intestinal inflammation, or gut microbiome composition and functioning. Our findings are important as they fill important knowledge gaps on the relative effectiveness of these widely used treatments. We are now investigating triple combination CFTR modulators with prolonged sampling periods.
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Affiliation(s)
- Ryan Marsh
- Department of Applied Sciences, Northumbria University, Newcastle, United Kingdom
| | - Claudio Dos Santos
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Liam Hanson
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Christabella Ng
- School of Medicine, University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Nottingham, United Kingdom
| | - Giles Major
- School of Medicine, University of Nottingham, Nottingham, United Kingdom
- Nestlé Institute of Health Sciences, Société des Produits Nestlé, Lausanne, Switzerland
| | - Alan R. Smyth
- School of Medicine, University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Nottingham, United Kingdom
| | - Damian Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Christopher van der Gast
- Department of Applied Sciences, Northumbria University, Newcastle, United Kingdom
- Department of Respiratory Medicine, Salford Royal NHS Foundation Trust, Salford, United Kingdom
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5
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Yang Y, Deng Y, Shi X, Liu L, Yin X, Zhao W, Li S, Yang C, Zhang T. QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification. WATER RESEARCH 2023; 235:119858. [PMID: 36931186 DOI: 10.1016/j.watres.2023.119858] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
The majority of the current regulatory practices for routine monitoring of beach water quality rely on the culture-based enumeration of faecal indicator bacteria (FIB) to develop criteria for promoting the general public's health. To address the limitations of culture methods and the arguable reliability of FIB in indicating health risks, we developed a Nanopore metagenomic sequencing-based viable cell absolute quantification workflow to rapidly and accurately estimate a broad range of microbes in beach waters by a combination of propidium monoazide (PMA) and cellular spike-ins. Using the simple synthetic bacterial communities mixed with viable and heat-killed cells, we observed near-complete relic DNA removal by PMA with minimal disturbance to the composition of viable cells, demonstrating the feasibility of PMA treatment in profiling viable cells by Nanopore sequencing. On a simple mock community comprised of 15 prokaryotic species, our results showed high accordance between the expected and estimated concentrations, suggesting the accuracy of our method in absolute quantification. We then further assessed the accuracy of our method for counting viable Escherichia coli and Vibrio spp. in beach waters by comparing to culture-based method, which were also in high agreement. Furthermore, we demonstrated that 1 Gb sequences obtained within 2 h would be sufficient to quantify a species having a concentration of ≥ 10 cells/mL in beach waters. Using our viability-resolved quantification workflow to assess the microbial risk of the beach water, we conducted (1) screening-level quantitative microbial risk assessment (QMRA) to investigate human illness risk and site-specific risk patterns that might guide risk management efforts and (2) metagenomics-based resistome risk assessment to evaluate another layer of risk caused by difficult illness treatment due to antimicrobial resistance (AMR). In summary, our metagenomic workflow for the rapid absolute quantification of viable bacteria demonstrated its great potential in paving new avenues toward holistic microbial risk assessment.
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Affiliation(s)
- Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Wanwan Zhao
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR, China.
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6
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Lin S, Ke Z, Lu M, Zhou Y, Tang W, Zhu S, Zhang Y, Li Z, Yin H, Chen Z. Specific labeling and identification of bacteria based on concentration-dependent carbon dot staining combined with hyperspectral imaging. JOURNAL OF BIOPHOTONICS 2023; 16:e202200237. [PMID: 36308004 DOI: 10.1002/jbio.202200237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/25/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Concentration-dependent carbon dot (CD) fluorescence was developed and utilized alongside hyperspectral microscopy as a specific labeling and identification technique for bacteria. Staining revealed that the CD concentration within cells depended on the characteristic intracellular environment of the species. Therefore, based on the concentration dependence of the CD fluorescence, different bacterial species were specifically labeled. Hyperspectral microscopy captured subtle fluorescence variations to identify bacteria. Method validation using Bacillus subtilis and Bacillus licheniformis succeeded with an identification accuracy of 99%. As a simple, rapid method for labeling and identifying bacterial species in mixtures, this technique has excellent potential for bacterial community studies.
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Affiliation(s)
- Sifan Lin
- Department of Optoelectronic Engineering, Jinan University, Guangzhou, China
| | - Ze Ke
- Department of Optoelectronic Engineering, Jinan University, Guangzhou, China
| | - Mingwei Lu
- Department of Optoelectronic Engineering, Jinan University, Guangzhou, China
| | - Yanzhong Zhou
- Department of Optoelectronic Engineering, Jinan University, Guangzhou, China
| | - Wenrui Tang
- Department of Optoelectronic Engineering, Jinan University, Guangzhou, China
| | - Siqi Zhu
- Guangdong Provincial Engineering Research Center of Crystal and Laser Technology, Guangzhou, China
| | - Yongqiang Zhang
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou, China
| | - Zhen Li
- Guangdong Provincial Engineering Research Center of Crystal and Laser Technology, Guangzhou, China
| | - Hao Yin
- Guangdong Provincial Engineering Research Center of Crystal and Laser Technology, Guangzhou, China
| | - Zhenqiang Chen
- Department of Optoelectronic Engineering, Jinan University, Guangzhou, China
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7
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Chakaroun R, Massier L, Musat N, Kovacs P. New Paradigms for Familiar Diseases: Lessons Learned on Circulatory Bacterial Signatures in Cardiometabolic Diseases. Exp Clin Endocrinol Diabetes 2022; 130:313-326. [PMID: 35320847 DOI: 10.1055/a-1756-4509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Despite the strongly accumulating evidence for microbial signatures in metabolic tissues, including the blood, suggesting a novel paradigm for metabolic disease development, the notion of a core blood bacterial signature in health and disease remains a contentious concept. Recent studies clearly demonstrate that under a strict contamination-free environment, methods such as 16 S rRNA gene sequencing, fluorescence in-situ hybridization, transmission electron microscopy, and several more, allied with advanced bioinformatics tools, allow unambiguous detection and quantification of bacteria and bacterial DNA in human tissues. Bacterial load and compositional changes in the blood have been reported for numerous disease states, suggesting that bacteria and their components may partially induce systemic inflammation in cardiometabolic disease. This concept has been so far primarily based on measurements of surrogate parameters. It is now highly desirable to translate the current knowledge into diagnostic, prognostic, and therapeutic approaches.This review addresses the potential clinical relevance of a blood bacterial signature pertinent to cardiometabolic diseases and outcomes and new avenues for translational approaches. It discusses pitfalls related to research in low bacterial biomass while proposing mitigation strategies for future research and application approaches.
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Affiliation(s)
- Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.,Wallenberg Laboratory, Department of Molecular and Clinical Medicine and Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, Gothenburg, Sweden
| | - Lucas Massier
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.,Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.,Deutsches Zentrum für Diabetesforschung eV, Neuherberg, Germany
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8
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Hockney R, Orr CH, Waring GJ, Christiaens I, Taylor G, Cummings SP, Robson SC, Nelson A. Formalin-Fixed Paraffin-Embedded (FFPE) samples are not a beneficial replacement for frozen tissues in fetal membrane microbiota research. PLoS One 2022; 17:e0265441. [PMID: 35298530 PMCID: PMC8929612 DOI: 10.1371/journal.pone.0265441] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Formalin-Fixed Paraffin-Embedded (FFPE) tissues are routinely collected, archived, and used for clinical diagnosis, including maternal and neonatal health. Applying FFPE samples to microbiota research would be beneficial to reduce preparation, storage and costs associated with limited available frozen samples. This research aims to understand if FFPE fetal membrane samples are comparable to frozen tissues, which are the current gold standard for DNA microbiota analysis. Extracted DNA from nine matched paired patients were sequenced by Illumina sequencing of the V4 16S rRNA gene region. This included duplicate frozen amnion and chorion fetal membrane rolls or FFPE combined amniochorionic samples. Negative controls of surrounding wax blocks and DNA extraction reagents were processed alongside samples using identical methods. DNA quality and quantity was assessed by NanoDrop, agarose gel electrophoresis and Bioanalyzer. Decontam and SourceTracker were integrated into microbiota analysis to identify the presence of contaminating sources. The bacterial profile and nine genera differed between FFPE and frozen fetal membranes. There were no differences in bacterial profiles between FFPE samples and corresponding wax negative controls, with 49% of bacteria in FFPE fetal membrane samples matched to the source origin of paraffin wax, and 40% originating from DNA extraction reagent sources. FFPE samples displayed high fragmentation and low quantity of extracted DNA compared to frozen samples. The microbiota of FFPE fetal membrane samples is influenced by processing methods, with the inability to differentiate between the microbiota of the tissue sample and the surrounding wax block. Illumina sequencing results of FFPE and frozen fetal membrane samples should not be compared using the methods employed here. Variation could be influenced by limitations including storage time, DNA extraction and purification methods. To utilise FFPE fetal membrane samples in microbiota research then contamination prevention and detection methods must be included into optimised and standardised protocols, with recommendations presented here.
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Affiliation(s)
- Rochelle Hockney
- School of Health, Leeds Beckett University, Leeds, United Kingdom
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
- * E-mail:
| | - Caroline H. Orr
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Gareth J. Waring
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Inge Christiaens
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Gillian Taylor
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Stephen P. Cummings
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, John Dixon Lane, Darlington, United Kingdom
| | - Stephen C. Robson
- Institute of Cellular Medicine, Newcastle University, Newcastle, United Kingdom
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
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9
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Hosokawa M, Endoh T, Kamata K, Arikawa K, Nishikawa Y, Kogawa M, Saeki T, Yoda T, Takeyama H. Strain-level profiling of viable microbial community by selective single-cell genome sequencing. Sci Rep 2022; 12:4443. [PMID: 35292746 PMCID: PMC8924182 DOI: 10.1038/s41598-022-08401-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/08/2022] [Indexed: 11/09/2022] Open
Abstract
Culture-independent analysis with high-throughput sequencing has been widely used to characterize bacterial communities. However, signals derived from non-viable bacteria and non-cell DNA may inhibit its characterization. Here, we present a method for viable bacteria-targeted single-cell genome sequencing, called PMA-SAG-gel, to obtain comprehensive whole-genome sequences of surviving uncultured bacteria from microbial communities. PMA-SAG-gel uses gel matrixes that enable sequential enzymatic reactions for cell lysis and genome amplification of viable single cells from the microbial communities. PMA-SAG-gel removed the single-amplified genomes (SAGs) derived from dead bacteria and enabled selective sequencing of viable bacteria in the model samples of Escherichia coli and Bacillus subtilis. Next, we demonstrated the recovery of near-complete SAGs of eight oxygen-tolerant bacteria, including Bacteroides spp. and Phocaeicola spp., from 1331 human feces SAGs. We found the presence of two different strains in each species and identified their specific genes to investigate the metabolic functions. The survival profile of an entire population at the strain level will provide the information for understanding the characteristics of the surviving bacteria under the specific environments or sample processing and insights for quality assessment of live bacterial products or fecal microbiota transplantation and for understanding the effect of antimicrobial treatments.
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Affiliation(s)
- Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan. .,Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan. .,bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan. .,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan. .,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
| | - Taruho Endoh
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Kazuma Kamata
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Koji Arikawa
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Yohei Nishikawa
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Masato Kogawa
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Tatsuya Saeki
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Takuya Yoda
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.,Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
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10
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Intestinal function and transit associate with gut microbiota dysbiosis in cystic fibrosis. J Cyst Fibros 2021; 21:506-513. [PMID: 34895838 DOI: 10.1016/j.jcf.2021.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/04/2021] [Accepted: 11/23/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Most people with cystic fibrosis (pwCF) suffer from gastrointestinal symptoms and are at risk of gut complications. Gut microbiota dysbiosis is apparent within the CF population across all age groups, with evidence linking dysbiosis to intestinal inflammation and other markers of health. This pilot study aimed to investigate the potential relationships between the gut microbiota and gastrointestinal physiology, transit, and health. STUDY DESIGN Faecal samples from 10 pwCF and matched controls were subject to 16S rRNA sequencing. Results were combined with clinical metadata and MRI metrics of gut function to investigate relationships. RESULTS pwCF had significantly reduced microbiota diversity compared to controls. Microbiota compositions were significantly different, suggesting remodelling of core and rarer satellite taxa in CF. Dissimilarity between groups was driven by a variety of taxa, including Escherichia coli, Bacteroides spp., Clostridium spp., and Faecalibacterium prausnitzii. The core taxa were explained primarily by CF disease, whilst the satellite taxa were associated with pulmonary antibiotic usage, CF disease, and gut function metrics. Species-specific ordination biplots revealed relationships between taxa and the clinical or MRI-based variables observed. CONCLUSIONS Alterations in gut function and transit resultant of CF disease are associated with the gut microbiota composition, notably the satellite taxa. Delayed transit in the small intestine might allow for the expansion of satellite taxa resulting in potential downstream consequences for core community function in the colon.
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11
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Legrand T, Wos‐Oxley M, Wynne J, Weyrich L, Oxley A. Dead or alive: microbial viability treatment reveals both active and inactive bacterial constituents in the fish gut microbiota. J Appl Microbiol 2021; 131:2528-2538. [PMID: 33945191 PMCID: PMC8596808 DOI: 10.1111/jam.15113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/22/2021] [Accepted: 04/17/2021] [Indexed: 12/26/2022]
Abstract
AIMS This study evaluated the microbial viability of fish gut microbiota in both digesta (faecal) and mucosal samples using a modified propidium monoazide (PMA) protocol, followed by 16S ribosomal RNA (rRNA) gene sequencing. METHODS AND RESULTS Digesta and gut mucosal samples from farmed yellowtail kingfish (Seriola lalandi) were collected and a modified PMA treatment was applied prior to DNA extraction to differentiate both active and nonviable microbial cells in the samples. All samples were then sequenced using a standard 16S rRNA approach. The digesta and mucosal samples contained significantly different bacterial communities, with a higher diversity observed in digesta samples. In addition, PMA treatment significantly reduced the microbial diversity and richness of digesta and mucosal samples and depleted bacterial constituents typically considered to be important within fish, such as Lactobacillales and Clostridales taxa. CONCLUSIONS These findings suggest that important bacterial members may not be active in the fish gut microbiota. In particular, several beneficial lactic acid bacteria (LAB) were identified as nonviable bacterial cells, potentially influencing the functional potential of the fish microbiota. SIGNIFICANCE AND IMPACTS OF THE STUDY Standardizing the methods for characterizing the fish microbiota are paramount in order to compare studies. In this study, we showed that both sample type and PMA treatment influence the bacterial communities found in the fish gut microbiota. Our findings also suggest that several microbes previously described in the fish gut may not be active constituents. As a result, these factors should be considered in future studies to better evaluate the active bacterial communities associated with the host.
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Affiliation(s)
- T.P.R.A. Legrand
- School of Biological SciencesThe University of AdelaideAdelaideSAAustralia
- CSIRO, Agriculture and FoodHobartTasAustralia
- South Australian Research and Development InstituteAquatic Sciences CentreWest BeachSAAustralia
| | - M.L. Wos‐Oxley
- College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
| | - J.W. Wynne
- CSIRO, Agriculture and FoodHobartTasAustralia
| | - L.S. Weyrich
- School of Biological SciencesThe University of AdelaideAdelaideSAAustralia
- Department of Anthropology and Huck Institutes of Life SciencesThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - A.P.A. Oxley
- Faculty of Science Engineering and Built EnvironmentSchool of Life and Environmental SciencesDeakin UniversityGeelongVic.Australia
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12
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Rustia AJ, Paterson JS, Best G, Sokoya EM. Microbial disruption in the gut promotes cerebral endothelial dysfunction. Physiol Rep 2021; 9:e15100. [PMID: 34755466 PMCID: PMC8578899 DOI: 10.14814/phy2.15100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/02/2021] [Indexed: 12/24/2022] Open
Abstract
Cerebrovascular disease is a group of conditions characterized by disorders of the cerebral vessels. Endothelial dysfunction renders the vasculature at risk of impaired blood flow and increases the potential of developing cerebrovascular disease. The gut microbiota has been recently identified as a possible risk factor of cerebrovascular disease. However, a direct link between gut microbiota and cerebral vascular function has not been established. Therefore, the aim of this study was to determine the effect of gut bacterial disruption on cerebral endothelial function. Male inbred Sprague-Dawley rats were randomly assigned to receive either drinking water with (n = 4) or without (n = 4) a cocktail of nonabsorbable broad-spectrum antibiotics (streptomycin, neomycin, bacitracin, and polymyxin B). Three weeks of antibiotic treatment resulted in a significant reduction in bacterial load and shifts within the bacterial sub-populations as assessed using flow cytometry. Using pressure myography, we found that spontaneous tone significantly increased and L-NAME-induced vasoconstriction was significantly blunted in middle cerebral arteries (MCAs) harvested from antibiotic-treated rats. ATP-mediated dilations were significantly blunted in MCAs from antibiotic-treated rats compared to their control counterparts. Immunoblotting revealed that the eNOS-P/total eNOS ratio was significantly reduced in cerebral artery lysates from antibiotic-treated rats compared to controls. Our findings suggest that disruption of the gut microbiota leads to cerebral endothelial dysfunction through reduction of eNOS activity. This study highlights the potential of the microbiota as a target to reverse endothelial dysfunction and a preventative approach to reducing risk of stroke and aneurysms.
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Affiliation(s)
- April J. Rustia
- Chronic Disease Research LaboratoryFlinders Health and Medical InstituteCollege of Medicine and Public HealthFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - James S. Paterson
- Microbial Systems LaboratoryCollege of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Giles Best
- Flow Cytometry FacilityFlinders Health and Medical Research InstituteCollege of Medicine and Public HealthFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Elke M. Sokoya
- Chronic Disease Research LaboratoryFlinders Health and Medical InstituteCollege of Medicine and Public HealthFlinders UniversityBedford ParkSouth AustraliaAustralia
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13
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Mancabelli L, Milani C, Anzalone R, Alessandri G, Lugli GA, Tarracchini C, Fontana F, Turroni F, Ventura M. Free DNA and Metagenomics Analyses: Evaluation of Free DNA Inactivation Protocols for Shotgun Metagenomics Analysis of Human Biological Matrices. Front Microbiol 2021; 12:749373. [PMID: 34691000 PMCID: PMC8527314 DOI: 10.3389/fmicb.2021.749373] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022] Open
Abstract
Culture-independent approaches now represent the gold standard for the investigation of both environmental and host-associated complex microbial communities. Nevertheless, despite the great advantages offered by these novel methodologies based on the use of next-generation DNA sequencing approaches, a number of bias sources have been identified. Among the latter, free DNA contained in biological matrices is one of the main sources of inaccuracy in reconstructing the resident microbial population of viable cells. For this reason, the photoreactive DNA-binding dye propidium monoazide (PMAxx™) has been developed by improving standard PMA. This compound binds and inactivates free DNA, thus preventing its amplification and sequencing. While the performances of PMA have been previously investigated, the efficiency with PMAxx™ has been tested mainly for amplicon-based profiling approaches on a limited number of biological matrices. In this study, we validated the performance of PMAxx™ for shotgun metagenomics approaches employing various human-associated matrices. Notably, results revealed that the effectiveness of PMAxx™ in inactivating free DNA of prokaryotes and eukaryotes tends to vary significantly based on the biological matrices analyzed.
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Affiliation(s)
- Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
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14
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Guo L, Wan K, Zhu J, Ye C, Chabi K, Yu X. Detection and distribution of vbnc/viable pathogenic bacteria in full-scale drinking water treatment plants. JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124335. [PMID: 33160785 DOI: 10.1016/j.jhazmat.2020.124335] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 05/22/2023]
Abstract
Viable but non-culturable (VBNC) bacteria have attracted widespread attention since they are inherently undetected by traditional culture-dependent methods. Importantly, VBNC bacteria could resuscitate under favorable conditions leading to significant public health concerns. Although the total number of viable bacteria has been theorized to be far greater than those that can be cultured, there have been no reports quantifying VBNC pathogenic bacteria in full-scale drinking water treatment plants (DWTPs). In this work, we used both culture-dependent and quantitative PCR combination with propidium monoazide (PMA) dye approaches to characterize cellular viability. Further, we established a method to quantify viable pathogens by relating specific gene copies to viable cell numbers. Ratios of culturable bacteria to viable 16S rRNA gene copies in water and biological activated carbon (BAC) biofilms were 0-4.75% and 0.04-56.24%, respectively. The VBNC E. coli, E. faecalis, P. aeruginosa, Salmonella sp., and Shigella sp. were detected at levels of 0-103 cells/100 mL in source water, 0-102 cells/100 mL in chlorinated water, and 0-103 cells/g in BAC biofilms. In addition, differences between the total and viable community structures after ozonation and chlorination were investigated. The relative abundance of opportunistic pathogens such as Mycobacterium, Sphingomonas, etc. increased in final water, likely due to their chlorine resistance. In summary, we detected significant quantities of viable/VBNC opportunistic pathogens in full-scale DWTPs, confirming that traditional, culture-dependent methods are inadequate for detecting VBNC bacteria. These findings suggest a need to develop and implement rapid, accurate methods for the detection of VBNC pathogenic bacteria in DWTPs to ensure the safety of drinking water.
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Affiliation(s)
- Lizheng Guo
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Wan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Chengsong Ye
- College of Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Kassim Chabi
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Yu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Environment & Ecology, Xiamen University, Xiamen 361102, China.
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15
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Marrs T, Jo JH, Perkin MR, Rivett DW, Witney AA, Bruce KD, Logan K, Craven J, Radulovic S, Versteeg SA, van Ree R, McLean WHI, Strachan DP, Lack G, Kong HH, Flohr C. Gut microbiota development during infancy: Impact of introducing allergenic foods. J Allergy Clin Immunol 2021; 147:613-621.e9. [PMID: 33551026 DOI: 10.1016/j.jaci.2020.09.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND The gut microbiota potentially plays an important role in the immunologic education of the host during early infancy. OBJECTIVE We sought to determine how the infant gut microbiota evolve during infancy, particularly in relation to hygiene-related environmental factors, atopic disorders, and a randomized introduction of allergenic solids. METHODS A total of 1303 exclusively breast-fed infants were enrolled in a dietary randomized controlled trial (Enquiring About Tolerance study) from 3 months of age. In this nested longitudinal study, fecal samples were collected at baseline, with additional sampling of selected cases and controls at 6 and 12 months to study the evolution of their gut microbiota, using 16S ribosomal RNA gene-targeted amplicon sequencing. RESULTS In the 288 baseline samples from exclusively breast-fed infant at 3 months, the gut microbiota was highly heterogeneous, forming 3 distinct clusters: Bifidobacterium-rich, Bacteroides-rich, and Escherichia/Shigella-rich. Mode of delivery was the major discriminating factor. Increased Clostridium sensu stricto relative abundance at 3 months was associated with presence of atopic dermatitis on examination at age 3 and 12 months. From the selected cases and controls with longitudinal samples (n = 70), transition to Bacteroides-rich communities and influx of adult-specific microbes were observed during the first year of life. The introduction of allergenic solids promoted a significant increase in Shannon diversity and representation of specific microbes, such as genera belonging to Prevotellaceae and Proteobacteria (eg, Escherichia/Shigella), as compared with infants recommended to exclusively breast-feed. CONCLUSIONS Specific gut microbiota characteristics of samples from 3-month-old breast-fed infants were associated with cesarean birth, and greater Clostridium sensu stricto abundance was associated with atopic dermatitis. The randomized introduction of allergenic solids from age 3 months alongside breast-feeding was associated with differential dynamics of maturation of the gut microbial communities.
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Affiliation(s)
- Tom Marrs
- Paediatric Allergy Research Group, Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom; Children's Allergies Department, Guy's and St Thomas' NHS Foundation Trust, St Thomas' Hospital, Lambeth, United Kingdom
| | - Jay-Hyun Jo
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Md
| | - Michael R Perkin
- Population Health Research Institute, St George's, University of London, London, United Kingdom
| | - Damian W Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St George's, University of London, London, United Kingdom
| | - Kenneth D Bruce
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Division, King's College London, London, United Kingdom
| | - Kirsty Logan
- Paediatric Allergy Research Group, Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Joanna Craven
- Paediatric Allergy Research Group, Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Suzana Radulovic
- Paediatric Allergy Research Group, Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom; Children's Allergies Department, Guy's and St Thomas' NHS Foundation Trust, St Thomas' Hospital, Lambeth, United Kingdom
| | - Serge A Versteeg
- Experimental Immunology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Ronald van Ree
- Experimental Immunology, Amsterdam University Medical Center, Amsterdam, The Netherlands; Department of Otorhinolaryngology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - W H Irwin McLean
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, United Kingdom
| | - Gideon Lack
- Paediatric Allergy Research Group, Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Md
| | - Carsten Flohr
- Unit for Population-Based Dermatology Research, St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom.
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16
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Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, Shen J, Vlamakis H, Hartmann EM, Huttenhower C. Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. MICROBIOME 2021; 9:17. [PMID: 33478576 PMCID: PMC7819323 DOI: 10.1186/s40168-020-00961-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/06/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g., qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting "viable" communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark "PMA-seq" (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. RESULTS PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis. However, in realistically complex communities (computer screens, computer mice, soil, and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability (even relative to variability in amplicon sequencing), with its performance largely affected by community properties such as initial biomass, sample types, and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the "PMA-responsive" microbes, we compared our results with previous PMA-based studies and found that PMA responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. CONCLUSIONS This study provides a comprehensive evaluation of PMA-seq exploring its quantitative potential in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities but provided only qualitative assessments in realistically complex community samples. Video abstract.
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Affiliation(s)
- Ya Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Kelsey N. Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Sena Bae
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Emma K. Accorsi
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
| | - Yancong Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
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17
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Nelson MT, Wolter DJ, Eng A, Weiss EJ, Vo AT, Brittnacher MJ, Hayden HS, Ravishankar S, Bautista G, Ratjen A, Blackledge M, McNamara S, Nay L, Majors C, Miller SI, Borenstein E, Simon RH, LiPuma JJ, Hoffman LR. Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome. Thorax 2020; 75:780-790. [PMID: 32631930 PMCID: PMC7875198 DOI: 10.1136/thoraxjnl-2019-214187] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 05/15/2020] [Accepted: 05/28/2020] [Indexed: 01/16/2023]
Abstract
RATIONALE The most common antibiotic used to treat people with cystic fibrosis (PWCF) is inhaled tobramycin, administered as maintenance therapy for chronic Pseudomonas aeruginosa lung infections. While the effects of inhaled tobramycin on P. aeruginosa abundance and lung function diminish with continued therapy, this maintenance treatment is known to improve long-term outcomes, underscoring how little is known about why antibiotics work in CF infections, what their effects are on complex CF sputum microbiomes and how to improve these treatments. OBJECTIVES To rigorously define the effect of maintenance tobramycin on CF sputum microbiome characteristics. METHODS AND MEASUREMENTS We collected sputum from 30 PWCF at standardised times before, during and after a single month-long course of maintenance inhaled tobramycin. We used traditional culture, quantitative PCR and metagenomic sequencing to define the dynamic effects of this treatment on sputum microbiomes, including abundance changes in both clinically targeted and untargeted bacteria, as well as functional gene categories. MAIN RESULTS CF sputum microbiota changed most markedly by 1 week of antibiotic therapy and plateaued thereafter, and this shift was largely driven by changes in non-dominant taxa. The genetically conferred functional capacities (ie, metagenomes) of subjects' sputum communities changed little with antibiotic perturbation, despite taxonomic shifts, suggesting functional redundancy within the CF sputum microbiome. CONCLUSIONS Maintenance treatment with inhaled tobramycin, an antibiotic with demonstrated long-term mortality benefit, primarily impacted clinically untargeted bacteria in CF sputum, highlighting the importance of monitoring the non-canonical effects of antibiotics and other treatments to accurately define and improve their clinical impact.
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Affiliation(s)
- Maria T Nelson
- Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington, United States
- Molecular and Cellular Biology, University of Washington School of Medicine, Seattle, Washington, United States
| | - Daniel J Wolter
- Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Alexander Eng
- Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Eli J Weiss
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Anh T Vo
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Hillary S Hayden
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Sumedha Ravishankar
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Gilbert Bautista
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Anina Ratjen
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Sharon McNamara
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Laura Nay
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
| | - Cheryl Majors
- Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Samuel I Miller
- Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States
| | - Elhanan Borenstein
- Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Richard H Simon
- Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - John J LiPuma
- Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Luke R Hoffman
- Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Pediatrics, Seattle Children's Hospital, Seattle, Washington, USA
- Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
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18
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D'Cruze N, Bates J, Assou D, Ronfot D, Coulthard E, Segniagbeto GH, Auliya M, Megson D, Rowntree J. A preliminary assessment of bacteria in “ranched” ball pythons (Python regius), Togo, West Africa. NATURE CONSERVATION 2020. [DOI: 10.3897/natureconservation.39.48599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Captive reptiles are routinely identified as reservoirs of pathogenic bacteria and reports of reptile-associated infections relating to some species are well documented (e.g., salmonellosis). Currently, relatively little is known about the epidemiology and bacteria of ball pythons. We carried out a survey of ball python farms in Togo, West Africa to assess the presence of any potentially pathogenic bacterial taxa that have been identified in recent scientific literature relating to this species. The presence of bacteria belonging to the genera Acinetobacter, Bacteroides, Citrobacter, Enterobacter, Lysobacter, Proteus, Pseudomonas, Staphylococcus, and Tsukamurella in oral and cloacal samples taken from five individual ball pythons is of potential concern for horizontal transmission given that pathogenic species belonging to these genera have been previously documented. The presence of bacteria belonging to the genera Clostridium, Escherichia, Moraxella, and Stenotrophomonas in the oral and rectal samples taken from five mice used to feed ball pythons suggests that they represent a potential reservoir of infection for wild caught ball pythons and their progeny. Furthermore, possible sources of environmental contamination include other captive amphibians, birds, reptiles and mammals, as well as free ranging birds and small mammals. Additional surveillance of ball pythons in the wild and in captivity at python farms in West Africa will shed light on whether or not this type of commercial activity is increasing pathogen exposure and lowering barriers to transmission. Meanwhile, as a precautionary measure, it is recommended that python farms should immediately establish biosecurity and disease surveillance practices to minimize potential horizontal and vertical bacterial transfer.
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19
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Nelson MT, Pope CE, Marsh RL, Wolter DJ, Weiss EJ, Hager KR, Vo AT, Brittnacher MJ, Radey MC, Hayden HS, Eng A, Miller SI, Borenstein E, Hoffman LR. Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles. Cell Rep 2020; 26:2227-2240.e5. [PMID: 30784601 PMCID: PMC6435281 DOI: 10.1016/j.celrep.2019.01.091] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/20/2018] [Accepted: 01/25/2019] [Indexed: 01/27/2023] Open
Abstract
Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. In addition, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. We describe a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. We show that this method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance. This finding underscores the substantial impact of DNA from sources other than live bacteria in micro-biological analyses of complex, chronic infection specimens. Nelson et al. describe a method for reducing both human cellular DNA and extracellular DNA (human and bacterial) in a complex respiratory sample using hypotonic lysis and endonuclease digestion. This method increases effective microbial sequencing depth and minimizes bias introduced into subsequent phylogenetic analysis by bacterial extracellular DNA.
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Affiliation(s)
- Maria T Nelson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA; Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Christopher E Pope
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Casuarina, NT 0811, Australia
| | - Daniel J Wolter
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Eli J Weiss
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Kyle R Hager
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Anh T Vo
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Mitchell J Brittnacher
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Matthew C Radey
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Hillary S Hayden
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Alexander Eng
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Samuel I Miller
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Computer Science and Engineering, University of Washington School of Medicine, Seattle, WA 98105, USA; Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA.
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20
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Cuthbertson L, Walker AW, Oliver AE, Rogers GB, Rivett DW, Hampton TH, Ashare A, Elborn JS, De Soyza A, Carroll MP, Hoffman LR, Lanyon C, Moskowitz SM, O’Toole GA, Parkhill J, Planet PJ, Teneback CC, Tunney MM, Zuckerman JB, Bruce KD, van der Gast CJ. Lung function and microbiota diversity in cystic fibrosis. MICROBIOME 2020; 8:45. [PMID: 32238195 PMCID: PMC7114784 DOI: 10.1186/s40168-020-00810-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/20/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Chronic infection and concomitant airway inflammation is the leading cause of morbidity and mortality for people living with cystic fibrosis (CF). Although chronic infection in CF is undeniably polymicrobial, involving a lung microbiota, infection surveillance and control approaches remain underpinned by classical aerobic culture-based microbiology. How to use microbiomics to direct clinical management of CF airway infections remains a crucial challenge. A pivotal step towards leveraging microbiome approaches in CF clinical care is to understand the ecology of the CF lung microbiome and identify ecological patterns of CF microbiota across a wide spectrum of lung disease. Assessing sputum samples from 299 patients attending 13 CF centres in Europe and the USA, we determined whether the emerging relationship of decreasing microbiota diversity with worsening lung function could be considered a generalised pattern of CF lung microbiota and explored its potential as an informative indicator of lung disease state in CF. RESULTS We tested and found decreasing microbiota diversity with a reduction in lung function to be a significant ecological pattern. Moreover, the loss of diversity was accompanied by an increase in microbiota dominance. Subsequently, we stratified patients into lung disease categories of increasing disease severity to further investigate relationships between microbiota characteristics and lung function, and the factors contributing to microbiota variance. Core taxa group composition became highly conserved within the severe disease category, while the rarer satellite taxa underpinned the high variability observed in the microbiota diversity. Further, the lung microbiota of individual patient were increasingly dominated by recognised CF pathogens as lung function decreased. Conversely, other bacteria, especially obligate anaerobes, increasingly dominated in those with better lung function. Ordination analyses revealed lung function and antibiotics to be main explanators of compositional variance in the microbiota and the core and satellite taxa. Biogeography was found to influence acquisition of the rarer satellite taxa. CONCLUSIONS Our findings demonstrate that microbiota diversity and dominance, as well as the identity of the dominant bacterial species, in combination with measures of lung function, can be used as informative indicators of disease state in CF. Video Abstract.
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Affiliation(s)
- Leah Cuthbertson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Alan W. Walker
- Rowett Institute, University of Aberdeen, Aberdeen, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Geraint B. Rogers
- South Australian Health and Medical Research Institute, Adelaide, Australia
- School of Medicine, Flinders University, Adelaide, Australia
| | - Damian W. Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Thomas H. Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH USA
| | - J. Stuart Elborn
- National Heart and Lung Institute, Imperial College London, London, UK
- Adult Cystic Fibrosis Department, Royal Brompton Hospital, London, UK
- School of Medicine, Dentistry and Biomedical Sciences, Institute for Health Sciences, Queen’s University Belfast, Belfast, UK
| | - Anthony De Soyza
- Institute of Cellular Medicine, NIHR Biomedical Research Centre for Ageing, Newcastle University, Newcastle, UK
- Department of Respiratory Medicine, Freeman Hospital, Newcastle, UK
| | - Mary P. Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - Lucas R. Hoffman
- Seattle Children’s Hospital, Seattle, WA USA
- Departments of Pediatrics and Microbiology, University of Washington, Seattle, WA USA
| | - Clare Lanyon
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle, UK
| | - Samuel M. Moskowitz
- Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, USA
- Vertex Pharmaceuticals, Boston, MA USA
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Julian Parkhill
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Paul J. Planet
- Pediatric Infectious Disease Division, Children’s Hospital of Philadelphia, Philadelphia, PA USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY USA
| | | | | | - Jonathan B. Zuckerman
- Maine Medical Center, Portland, ME USA
- School of Medicine, Tufts University, Boston, MA USA
| | - Kenneth D. Bruce
- Institute of Pharmaceutical Science, King’s College London, London, UK
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21
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Bacterial dominance is due to effective utilisation of secondary metabolites produced by competitors. Sci Rep 2020; 10:2316. [PMID: 32047185 PMCID: PMC7012823 DOI: 10.1038/s41598-020-59048-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/08/2020] [Indexed: 12/23/2022] Open
Abstract
Interactions between bacteria govern the progression of respiratory infections; however, the mechanisms underpinning these interactions are still unclear. Understanding how a bacterial species comes to dominate infectious communities associated with respiratory infections has direct relevance to treatment. In this study, Burkholderia, Pseudomonas, and Staphylococcus species were isolated from the sputum of an individual with Cystic Fibrosis and assembled in a fully factorial design to create simple microcosms. Measurements of growth and habitat modification were recorded over time, the later using proton Nuclear Magnetic Resonance spectra. The results showed interactions between the bacteria became increasingly neutral over time. Concurrently, the bacteria significantly altered their ability to modify the environment, with Pseudomonas able to utilise secondary metabolites produced by the other two isolates, whereas the reverse was not observed. This study indicates the importance of including data about the habitat modification of a community, to better elucidate the mechanisms of bacterial interactions.
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22
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O'Callaghan JL, Turner R, Dekker Nitert M, Barrett HL, Clifton V, Pelzer ES. Re-assessing microbiomes in the low-biomass reproductive niche. BJOG 2019; 127:147-158. [PMID: 31587490 DOI: 10.1111/1471-0528.15974] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 12/21/2022]
Abstract
The female reproductive tract represents a continuum between the vagina and the upper genital tract. New evidence from cultivation-independent studies suggests that the female upper genital tract is not sterile; however, the significance of this for reproductive health and disease remains to be elucidated fully. Further, diagnosis and treatment of infectious reproductive tract pathologies using cultivation-independent technologies represents a largely unchartered area of modern medical science. The challenge now is to design well-controlled experiments to account for the ease of contamination known to confound molecular-based studies of low-biomass niches, including the uterus and placenta. This will support robust assessment of the potential function of microorganisms, microbial metabolites, and cell-free bacterial DNA on reproductive function in health and disease. TWEETABLE ABSTRACT: Molecular microbial studies of low-biomass niches require stringent experimental controls to reveal causal relations in reproductive health and disease.
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Affiliation(s)
- J L O'Callaghan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia.,Institute of Health and Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia
| | - R Turner
- The Wesley Hospital, Auchenflower, Qld, Australia
| | - M Dekker Nitert
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, St Lucia, Qld, Australia
| | - H L Barrett
- Endocrinology, Mater Hospital, South Brisbane, Qld, Australia.,Mater Research, University of Queensland, St Lucia, Qld, Australia
| | - V Clifton
- Mater Research, Pregnancy and Development Group, South Brisbane, Qld, Australia
| | - E S Pelzer
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia.,Institute of Health and Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia
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23
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Naidoo CC, Nyawo GR, Wu BG, Walzl G, Warren RM, Segal LN, Theron G. The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda. THE LANCET. RESPIRATORY MEDICINE 2019; 7:892-906. [PMID: 30910543 DOI: 10.1016/s2213-2600(18)30501-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 01/26/2023]
Abstract
The diverse microbial communities within our bodies produce metabolites that modulate host immune responses. Even the microbiome at distal sites has an important function in respiratory health. However, the clinical importance of the microbiome in tuberculosis, the biggest infectious cause of death worldwide, is only starting to be understood. Here, we critically review research on the microbiome's association with pulmonary tuberculosis. The research indicates five main points: (1) susceptibility to infection and progression to active tuberculosis is altered by gut Helicobacter co-infection, (2) aerosol Mycobacterium tuberculosis infection changes the gut microbiota, (3) oral anaerobes in the lung make metabolites that decrease pulmonary immunity and predict progression, (4) the increased susceptibility to reinfection of patients who have previously been treated for tuberculosis is likely due to the depletion of T-cell epitopes on commensal gut non-tuberculosis mycobacteria, and (5) the prolonged antibiotic treatment required for cure of tuberculosis has long-term detrimental effects on the microbiome. We highlight knowledge gaps, considerations for addressing these knowledge gaps, and describe potential targets for modifying the microbiome to control tuberculosis.
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Affiliation(s)
- Charissa C Naidoo
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Georgina R Nyawo
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Gerhard Walzl
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Grant Theron
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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24
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A longitudinal characterization of the Non-Cystic Fibrosis Bronchiectasis airway microbiome. Sci Rep 2019; 9:6871. [PMID: 31053725 PMCID: PMC6499777 DOI: 10.1038/s41598-019-42862-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 04/08/2019] [Indexed: 12/30/2022] Open
Abstract
A diverse microbiota exists within the airways of individuals with non-cystic fibrosis bronchiectasis (nCFB). How the lung microbiome evolves over time, and whether changes within the microbiome correlate with future disease progression is not yet known. We assessed the microbial community structure of 133 serial sputa and subsequent disease course of 29 nCFB patients collected over a span of 4–16 years using 16S rRNA paired-end sequencing. Interestingly, no significant shifts in the microbial community of individuals were observed during extended follow-up suggesting the microbiome remains relatively stable over prolonged periods. Samples that were Pseudomonas aeruginosa culture positive displayed markedly different microbial community structures compared to those that were positive for Haemophilus influenzae. Importantly, patients with sputum of lower microbial community diversity were more likely to experience subsequent lung function decline as defined by annual change in ≥−1 FEV1% predicted. Shannon diversity values <1 were more prevalent in patients with FEV1 decline (P = 0.002). However, the relative abundance of particular core microbiota constituents did not associate with risk of decline. Here we present data confirming that the microbiome of nCFB individuals is generally stable, and that microbiome-based measurements may have a prognostic role as biomarkers for nCFB.
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25
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Stinson LF, Keelan JA, Payne MS. Characterization of the bacterial microbiome in first-pass meconium using propidium monoazide (PMA) to exclude nonviable bacterial DNA. Lett Appl Microbiol 2019; 68:378-385. [PMID: 30674082 DOI: 10.1111/lam.13119] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/29/2022]
Abstract
Numerous studies have reported bacterial DNA in first-pass meconium samples, suggesting that the human gut microbiome is seeded prior to birth. However, these studies have not been able to discriminate between DNA from living bacterial cells, DNA from dead bacterial cells or cell-free DNA. Here we have used propidium monoazide (PMA) together with 16S rRNA gene sequencing to determine whether there are intact bacterial cells in the fetal gut. DNA was extracted from first-pass meconium (n = 5) and subjected to 16S rRNA gene sequencing with/without PMA treatment. All meconium samples, regardless of PMA treatment, contained detectable levels of bacterial DNA; however, treatment with PMA prior to DNA extraction decreased the DNA yield by approximately 20%. PMA-treated meconium samples did not differ significantly from untreated samples in terms of observed number of OTUs (P = 0·945); although they did differ taxonomically, with around one quarter of OTUs identified in untreated samples only, suggesting that they have originated from cell-free/nonviable DNA. The mean Sørensen coefficient for treated vs untreated samples was 0·527. Our findings suggest that the fetal gut is seeded with intact bacterial cells prior to birth. This is an important finding, as exposure to live bacteria during gestation might have a significant impact on the developing fetus. SIGNIFICANCE AND IMPACT OF THE STUDY: DNA-based microbiome studies performed using 16S rRNA gene sequencing are limited by their inability to discriminate between live bacterial cells, dead bacterial cells and cell-free DNA. Here we use propidium monoazide (PMA) to exclude nonviable bacteria from microbiome analysis of first-pass meconium samples and thereby reveal that the majority of the purported fetal gut microbiome is from intact bacterial cells. This work demonstrates the importance of excluding nonviable bacteria when analysing the microbial community in low-biomass samples such as meconium.
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Affiliation(s)
- L F Stinson
- Division of Obstetrics and Gynaecology, Faculty of Health & Medical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - J A Keelan
- Division of Obstetrics and Gynaecology, Faculty of Health & Medical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - M S Payne
- Division of Obstetrics and Gynaecology, Faculty of Health & Medical Sciences, The University of Western Australia, Crawley, WA, Australia
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26
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Agustí G, Codony F. Commentary: Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis. Front Cell Infect Microbiol 2018; 8:212. [PMID: 29974038 PMCID: PMC6020329 DOI: 10.3389/fcimb.2018.00212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 06/05/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Gemma Agustí
- Departament d'Òptica i Optometria, Universitat Politècnica de Catalunya-Barcelona Tech, Terrassa, Spain
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27
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The lung microbiome. Emerg Top Life Sci 2017; 1:313-324. [PMID: 33525774 DOI: 10.1042/etls20170043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022]
Abstract
Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.
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28
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Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. MICROBIOME 2017; 5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
Abstract
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.
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Affiliation(s)
- Joanne B. Emerson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 USA
- Current Address: Department of Plant Pathology, University of California, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Clarisse M. Betancourt Román
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Brandon Brooks
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720 USA
| | - David A. Coil
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Katherine Dahlhausen
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Holly H. Ganz
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Tiffany Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Nicholas B. Justice
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
| | - Ivan G. Paulino-Lima
- Universities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA 94035-1000 USA
| | - Julia C. Luongo
- Department of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO 80309 USA
| | - Despoina S. Lymperopoulou
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Cinta Gomez-Silvan
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94702 USA
| | | | - Melike Balk
- Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Andreas Nocker
- IWW Water Centre, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Lynn J. Rothschild
- Planetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA 94035-1000 USA
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Howlin RP, Cathie K, Hall-Stoodley L, Cornelius V, Duignan C, Allan RN, Fernandez BO, Barraud N, Bruce KD, Jefferies J, Kelso M, Kjelleberg S, Rice SA, Rogers GB, Pink S, Smith C, Sukhtankar PS, Salib R, Legg J, Carroll M, Daniels T, Feelisch M, Stoodley P, Clarke SC, Connett G, Faust SN, Webb JS. Low-Dose Nitric Oxide as Targeted Anti-biofilm Adjunctive Therapy to Treat Chronic Pseudomonas aeruginosa Infection in Cystic Fibrosis. Mol Ther 2017; 25:2104-2116. [PMID: 28750737 PMCID: PMC5589160 DOI: 10.1016/j.ymthe.2017.06.021] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/23/2017] [Accepted: 06/24/2017] [Indexed: 12/31/2022] Open
Abstract
Despite aggressive antibiotic therapy, bronchopulmonary colonization by Pseudomonas aeruginosa causes persistent morbidity and mortality in cystic fibrosis (CF). Chronic P. aeruginosa infection in the CF lung is associated with structured, antibiotic-tolerant bacterial aggregates known as biofilms. We have demonstrated the effects of non-bactericidal, low-dose nitric oxide (NO), a signaling molecule that induces biofilm dispersal, as a novel adjunctive therapy for P. aeruginosa biofilm infection in CF in an ex vivo model and a proof-of-concept double-blind clinical trial. Submicromolar NO concentrations alone caused disruption of biofilms within ex vivo CF sputum and a statistically significant decrease in ex vivo biofilm tolerance to tobramycin and tobramycin combined with ceftazidime. In the 12-patient randomized clinical trial, 10 ppm NO inhalation caused significant reduction in P. aeruginosa biofilm aggregates compared with placebo across 7 days of treatment. Our results suggest a benefit of using low-dose NO as adjunctive therapy to enhance the efficacy of antibiotics used to treat acute P. aeruginosa exacerbations in CF. Strategies to induce the disruption of biofilms have the potential to overcome biofilm-associated antibiotic tolerance in CF and other biofilm-related diseases.
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Affiliation(s)
- Robert P Howlin
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Katrina Cathie
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Luanne Hall-Stoodley
- Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH 43210-2210, USA; Southampton NIHR Wellcome Trust Clinical Research Facility, Southampton SO16 6YD, UK
| | - Victoria Cornelius
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; Imperial College London School of Public Health, London SW7 2AZ, UK
| | - Caroline Duignan
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Raymond N Allan
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO17 1BJ, UK; Southampton NIHR Wellcome Trust Clinical Research Facility, Southampton SO16 6YD, UK
| | - Bernadette O Fernandez
- Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Nicolas Barraud
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ken D Bruce
- Kings College London Institute of Pharmaceutical Science, London WC2R 2LS, UK
| | - Johanna Jefferies
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO17 1BJ, UK; Public Health England, Southampton SO17 1BJ, UK
| | - Michael Kelso
- Illawarra Health and Medical Research Institute and School of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Staffan Kjelleberg
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Singapore Centre on Environmental Life Sciences Engineering and Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Scott A Rice
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Singapore Centre on Environmental Life Sciences Engineering and Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Geraint B Rogers
- Kings College London Institute of Pharmaceutical Science, London WC2R 2LS, UK; Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; Flinders University School of Medicine, Bedford Park, Adelaide, SA 5042, Australia
| | - Sandra Pink
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK
| | - Caroline Smith
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK
| | - Priya S Sukhtankar
- Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO17 1BJ, UK; Southampton NIHR Wellcome Trust Clinical Research Facility, Southampton SO16 6YD, UK
| | - Rami Salib
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Julian Legg
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK
| | - Mary Carroll
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK
| | - Thomas Daniels
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK
| | - Martin Feelisch
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Paul Stoodley
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Microbial Infection and Immunity, The Ohio State University College of Medicine, Columbus, OH 43210-2210, USA; National Centre for Advanced Tribology at Southampton, Faculty of Engineering, University of Southampton, Southampton SO17 1BJ, UK
| | - Stuart C Clarke
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO17 1BJ, UK; Public Health England, Southampton SO17 1BJ, UK
| | - Gary Connett
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK
| | - Saul N Faust
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO17 1BJ, UK; Southampton NIHR Wellcome Trust Clinical Research Facility, Southampton SO16 6YD, UK.
| | - Jeremy S Webb
- NIHR Southampton Respiratory Biomedical Research Centre, Southampton SO16 6YD, UK; University Hospital Southampton NHS Foundation Trust, Southampton SO16, 6YD, UK; Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
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Young GR, Smith DL, Embleton ND, Berrington JE, Schwalbe EC, Cummings SP, van der Gast CJ, Lanyon C. Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis. Front Cell Infect Microbiol 2017. [PMID: 28634574 PMCID: PMC5459914 DOI: 10.3389/fcimb.2017.00237] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Necrotising enterocolitis (NEC) and sepsis are serious diseases of preterm infants that can result in feeding intolerance, the need for bowel resection, impaired physiological and neurological development, and high mortality rates. Neonatal healthcare improvements have allowed greater survival rates in preterm infants leading to increased numbers at risk of developing NEC and sepsis. Gut bacteria play a role in protection from or propensity to these conditions and have therefore, been studied extensively using targeted 16S rRNA gene sequencing methods. However, exact epidemiology of these conditions remain unknown and the role of the gut microbiota in NEC remains enigmatic. Many studies have confounding variables such as differing clinical intervention strategies or major methodological issues such as the inability of 16S rRNA gene sequencing methods to determine viable from non-viable taxa. Identification of viable community members is important to identify links between the microbiota and disease in the highly unstable preterm infant gut. This is especially important as remnant DNA is robust and persists in the sampling environment following cell death. Chelation of such DNA prevents downstream amplification and inclusion in microbiota characterisation. This study validates use of propidium monoazide (PMA), a DNA chelating agent that is excluded by an undamaged bacterial membrane, to reduce bias associated with 16S rRNA gene analysis of clinical stool samples. We aim to improve identification of the viable microbiota in order to increase the accuracy of clinical inferences made regarding the impact of the preterm gut microbiota on health and disease. Gut microbiota analysis was completed on stools from matched twins (n = 16) that received probiotics. Samples were treated with PMA, prior to bacterial DNA extraction. Meta-analysis highlighted a significant reduction in bacterial diversity in 68.8% of PMA treated samples as well as significantly reduced overall rare taxa abundance. Importantly, overall abundances of genera associated with protection from and propensity to NEC and sepsis such as: Bifidobacterium; Clostridium, and Staphylococcus sp. were significantly different following PMA-treatment. These results suggest non-viable cell exclusion by PMA-treatment reduces bias in gut microbiota analysis from which clinical inferences regarding patient susceptibility to NEC and sepsis are made.
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Affiliation(s)
- Gregory R Young
- Faculty of Health and Life Sciences, University of NorthumbriaNewcastle upon Tyne, United Kingdom
| | - Darren L Smith
- Faculty of Health and Life Sciences, University of NorthumbriaNewcastle upon Tyne, United Kingdom
| | - Nicholas D Embleton
- Newcastle Neonatal Service, Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon Tyne, United Kingdom
| | - Janet E Berrington
- Newcastle Neonatal Service, Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon Tyne, United Kingdom
| | - Edward C Schwalbe
- Faculty of Health and Life Sciences, University of NorthumbriaNewcastle upon Tyne, United Kingdom
| | - Stephen P Cummings
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | | | - Clare Lanyon
- Faculty of Health and Life Sciences, University of NorthumbriaNewcastle upon Tyne, United Kingdom
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31
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Xie Y, Qiu N, Wang G. Toward a better guard of coastal water safety-Microbial distribution in coastal water and their facile detection. MARINE POLLUTION BULLETIN 2017; 118:5-16. [PMID: 28215556 DOI: 10.1016/j.marpolbul.2017.02.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 01/19/2017] [Accepted: 02/09/2017] [Indexed: 06/06/2023]
Abstract
Prosperous development in marine-based tourism has raised increasing concerns over the sanitary quality of coastal waters with potential microbial contamination. The World Health Organization has set stringent standards over a list of pathogenic microorganisms posing potential threats to people with frequent coastal water exposure and has asked for efficient detection procedures for pathogen facile identification. Inspection of survey events regarding the occurrence of marine pathogens in recreational beaches in recent years has reinforced the need for the development of a rapid identification procedure. In this review, we examine the possibility of recruiting uniform molecular assays to identify different marine pathogens and the feasibility of appropriate biomarkers, including enterochelin biosynthetic genes, for general toxicity assays. The focus is not only on bacterial pathogens but also on other groups of infectious pathogens. The ultimate goal is the development of a handy method to more efficiently and rapidly detect marine pathogens.
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Affiliation(s)
- Yunxuan Xie
- Tianjin University Center for Marine Environmental Ecology, School of Environmental Science & Engineering, Tianjin University, Tianjin 300072, China
| | - Ning Qiu
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Guangyi Wang
- Tianjin University Center for Marine Environmental Ecology, School of Environmental Science & Engineering, Tianjin University, Tianjin 300072, China.
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32
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Detection of Viable Bacteria during Sludge Ozonation by the Combination of ATP Assay with PMA-Miseq Sequencing. WATER 2017. [DOI: 10.3390/w9030166] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Using sludge obtained from municipal sewage treatment plants, the response of viable bacterial populations during the sludge ozonation process was investigated by a combination of adenosine triphosphate (ATP) assay and propidium monoazide (PMA)-Miseq sequencing. The ATP assay was first optimized for application on sludge samples by adjusting the sludge solid contents and reaction time. PMA-modified polymerase chain reaction (PCR) was also optimized by choosing the suitable final PMA concentration. The quantity and composition of viable bacterial populations during sludge ozonation were further elucidated using the optimized ATP and PMA-modified PCR methods. The results indicated that after the sludge was exposed to ozone (O3) at 135 mg·O3/g total suspended solids (TSS), the viable biomass displayed a substantial decrease, with a reduction rate reaching 70.89%. The composition of viable bacterial communities showed a faster succession, showing that an ozone dosage of 114 mg·O3/g TSS is enough to significantly change the viable bacterial population structure. Floc-forming genera, such as Zoogloea, Ferruginibacter, Thauera and Turneriella, are sensitive to ozonation, while the relative abundances of some functional bacterial genera, including SM1A02, Nitrospira and Candidatus Accumulibacter, remained constant or increased in the viable bacterial population during sludge ozonation, indicating that they are more resistant to ozonation.
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Nguyen LDN, Deschaght P, Merlin S, Loywick A, Audebert C, Van Daele S, Viscogliosi E, Vaneechoutte M, Delhaes L. Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation. PLoS One 2016; 11:e0168860. [PMID: 28030619 PMCID: PMC5193350 DOI: 10.1371/journal.pone.0168860] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 12/07/2016] [Indexed: 02/06/2023] Open
Abstract
Introduction and Purpose Propidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine whether a PMA-pretreatment coupled with high-throughput sequencing analysis provides a different picture of the airway mycobiome and bacteriome. Results and Discussion We compared deep-sequencing data of mycobiota and microbiota of 15 sputum samples from 5 cystic fibrosis (CF) patients with and without prior PMA-treatment of the DNA-extracts. PMA-pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic units (OTUs) with a relative abundance greater than or equal to 1%), but caused a significant difference in the intermediate community (less than 1%) when analyzing the alpha biodiversity Simpson index (p = 0.03). Regarding PMA impact on the airway mycobiota evaluated for the first time here; no significant differences in alpha diversity indexes between PMA-treated and untreated samples were observed. Regarding beta diversity analysis, the intermediate communities also differed more dramatically than the total and abundant ones when studying both mycobiome and bacteriome. Our results showed that only the intermediate (or low abundance) population diversity is impacted by PMA-treatment, and therefore that abundant taxa are mostly viable during acute exacerbation in CF. Given such a cumbersome protocol (PMA-pretreatment coupled with high-throughput sequencing), we discuss its potential interest within the follow-up of CF patients. Further studies using PMA-pretreatment are warranted to improve our “omic” knowledge of the CF airways.
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Affiliation(s)
- Linh Do Ngoc Nguyen
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France
| | - Pieter Deschaght
- Laboratory for Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Sophie Merlin
- GenesDiffusion, Douai, France
- PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France
| | - Alexandre Loywick
- GenesDiffusion, Douai, France
- PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France
| | - Christophe Audebert
- GenesDiffusion, Douai, France
- PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France
| | - Sabine Van Daele
- Department of Pediatrics and Genetics, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Eric Viscogliosi
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France
| | - Mario Vaneechoutte
- Laboratory for Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Laurence Delhaes
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France
- Parasitology-Medical Mycology Department, Regional Hospital Center, Faculty of Medicine, Lille, France
- * E-mail:
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Kowalczyk A, Price OR, van der Gast CJ, Finnegan CJ, van Egmond RA, Schäfer H, Bending GD. Spatial and temporal variability in the potential of river water biofilms to degrade p-nitrophenol. CHEMOSPHERE 2016; 164:355-362. [PMID: 27596822 DOI: 10.1016/j.chemosphere.2016.08.095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/14/2016] [Accepted: 08/20/2016] [Indexed: 06/06/2023]
Abstract
In order to predict the fate of chemicals in the environment, a range of regulatory tests are performed with microbial inocula collected from environmental compartments to investigate the potential for biodegradation. The abundance and distribution of microbes in the environment is affected by a range of variables, hence diversity and biomass of inocula used in biodegradation tests can be highly variable in space and time. The use of artificial or natural biofilms in regulatory tests could enable more consistent microbial communities be used as inocula, in order to increase test consistency. We investigated spatial and temporal variation in composition, biomass and chemical biodegradation potential of bacterial biofilms formed in river water. Sampling time and sampling location impacted the capacity of biofilms to degrade p-nitrophenol (PNP). Biofilm bacterial community structure varied across sampling times, but was not affected by sampling location. Degradation of PNP was associated with increased relative abundance of Pseudomonas syringae. Partitioning of the bacterial metacommunity into core and satellite taxa revealed that the P. syringae could be either a satellite or core member of the community across sampling times, but this had no impact on PNP degradation. Quantitative PCR analysis of the pnpA gene showed that it was present in all samples irrespective of their ability to degrade PNP. River biofilms showed seasonal variation in biomass, microbial community composition and PNP biodegradation potential, which resulted in inconsistent biodegradation test results. We discuss the results in the context of the mechanisms underlying variation in regulatory chemical degradation tests.
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Affiliation(s)
- Agnieszka Kowalczyk
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK.
| | - Oliver R Price
- Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Christopher J van der Gast
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK; NERC Centre for Ecology and Hydrology, Wallingford, OX10 8BB, UK
| | - Christopher J Finnegan
- Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Roger A van Egmond
- Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Hendrik Schäfer
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - Gary D Bending
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
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Evaluation of quantitative PCR for early diagnosis of Pseudomonas aeruginosa infection in cystic fibrosis: a prospective cohort study. Clin Microbiol Infect 2016; 23:203-207. [PMID: 27903460 DOI: 10.1016/j.cmi.2016.11.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/31/2016] [Accepted: 11/22/2016] [Indexed: 01/29/2023]
Abstract
OBJECTIVES Early detection of Pseudomonas aeruginosa lung positivity is a key element in cystic fibrosis (CF) management. PCR has increased the accuracy of detection of many microorganisms. Clinical relevance of P. aeruginosa quantitative PCR (qPCR) in this context is unclear. Our aim was to determine P. aeruginosa qPCR sensitivity and specificity, and to assess the possible time saved by qPCR in comparison with standard practice (culture). METHODS A multicentre cohort study was conducted over a 3-year period in 96 patients with CF without chronic P. aeruginosa colonization. Sputum samples were collected at each visit. Conventional culture and two-step qPCR (oprL qPCR and gyrB/ecfX qPCR) were performed for 707 samples. The positivity criteria were based on the qPCR results, defined in a previous study as follow: oprL qPCR positivity alone if bacterial density was <730 CFU/mL or oprL qPCR combined with gyrB/ecfX qPCR if bacterial density was ≥730 CFU/mL. RESULTS During follow up, 36 of the 96 patients with CF were diagnosed on culture as colonized with P. aeruginosa. This two-step qPCR displayed a sensitivity of 94.3% (95% CI 79.7%-98.6%), and a specificity of 86.3% (95% CI 83.4%-88.7%). It enabled P. aeruginosa acquisition to be diagnosed earlier in 20 patients, providing a median detection time gain of 8 months (interquartile range 3.7-17.6) for them. CONCLUSIONS Implementing oprL and gyrB/ecfX qPCR in the management of patients with CF allowed earlier detection of first P. aeruginosa lung positivity than culture alone.
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Jo JH, Kennedy EA, Kong HH. Topographical and physiological differences of the skin mycobiome in health and disease. Virulence 2016; 8:324-333. [PMID: 27754756 DOI: 10.1080/21505594.2016.1249093] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Skin constantly encounters external elements, including microbes. Culture-based studies have identified fungi present on human skin and have linked some species with certain skin diseases. Moreover, modern medical treatments, especially immunosuppressants, have increased the population at risk for cutaneous and invasive fungal infections, emphasizing the need to understand skin fungal communities in health and disease. A major hurdle for studying fungal flora at a community level has been the heterogeneous culture conditions required by skin fungi. Recent advances in DNA sequencing technologies have dramatically expanded our knowledge of the skin microbiome through culture-free methods. This review discusses historical and recent research on skin fungal communities - the mycobiome - in health and disease, and challenges associated with sequencing-based mycobiome research.
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Affiliation(s)
- Jay-Hyun Jo
- a Dermatology Branch, Center for Cancer Research , National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
| | - Elizabeth A Kennedy
- a Dermatology Branch, Center for Cancer Research , National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
| | - Heidi H Kong
- a Dermatology Branch, Center for Cancer Research , National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
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Hauptmann M, Schaible UE. Linking microbiota and respiratory disease. FEBS Lett 2016; 590:3721-3738. [PMID: 27637588 DOI: 10.1002/1873-3468.12421] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/30/2016] [Accepted: 09/07/2016] [Indexed: 12/13/2022]
Abstract
An increasing body of evidence indicates the relevance of microbiota for pulmonary health and disease. Independent investigations recently demonstrated that the lung harbors a resident microbiota. Therefore, it is intriguing that a lung microbiota can shape pulmonary immunity and epithelial barrier functions. Here, we discuss the ways how the composition of the microbial community in the lung may influence pulmonary health and vice versa, factors that determine community composition. Prominent microbiota at other body sites such as the intestinal one may also contribute to pulmonary health and disease. However, it is difficult to discriminate between influences of lung vs. gut microbiota due to systemic mutuality between both communities. With focuses on asthma and respiratory infections, we discuss how microbiota of lung and gut can determine pulmonary immunity and barrier functions.
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Affiliation(s)
- Matthias Hauptmann
- Priority Program Infections, Cellular Microbiology, Research Center Borstel, Germany
| | - Ulrich E Schaible
- Priority Program Infections, Cellular Microbiology, Research Center Borstel, Germany.,German Centre for Infection Research, TTU-TB, Borstel, Germany
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Zhao F, Liu H, Zhang Z, Xiao L, Sun X, Xie J, Pan Y, Zhao Y. Reducing bias in complex microbial community analysis in shrimp based on propidium monoazide combined with PCR-DGGE. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.03.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? Ann Am Thorac Soc 2016; 12 Suppl 2:S207-11. [PMID: 26595741 DOI: 10.1513/annalsats.201506-353aw] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pulmonary exacerbations account for much of the decrease in lung function and consequently most of the morbidity and mortality in patients with cystic fibrosis. These events are driven by an acute inflammatory response to infection. Recent technological advancements in molecular profiling techniques have allowed for a proliferation of microbiome studies of the lower airways of patients with cystic fibrosis. But these methods may not provide a comprehensive and unbiased measure of the lung microbiota in these patients and molecular profiles do not always translate to quantitative microbiology. Furthermore, these studies have not yet been able to provide much in the way of mechanistic insights into exacerbations or to guide patient therapy. We propose a model in which pulmonary exacerbations may be driven by an active subpopulation of the lung microbiota, which may represent only a small portion of the microbiota measured in a clinical sample. Methodology should be focused on the ultimate goal, which is to use the best available approaches to provide accurate quantitative measures of the microbiome to inform clinical decisions and provide rapid assessment of treatment efficacy. These strategies would be relevant to other chronic lung diseases such as chronic obstructive pulmonary disease and neutrophilic asthma.
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Abstract
There are a range of methodologies available to study the human microbiota, ranging from traditional approaches such as culturing through to state-of-the-art developments in next generation DNA sequencing technologies. The advent of molecular techniques in particular has opened up tremendous new avenues for research, and has galvanised interest in the study of our microbial inhabitants. Given the dazzling array of available options, however, it is important to understand the inherent advantages and limitations of each technique so that the best approach can be employed to address the particular research objective. In this chapter we cover some of the most widely used current techniques in human microbiota research and highlight the particular strengths and caveats associated with each approach.
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Affiliation(s)
- Alan W Walker
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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Bacci G, Paganin P, Lopez L, Vanni C, Dalmastri C, Cantale C, Daddiego L, Perrotta G, Dolce D, Morelli P, Tuccio V, De Alessandri A, Fiscarelli EV, Taccetti G, Lucidi V, Bevivino A, Mengoni A. Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline. PLoS One 2016; 11:e0156807. [PMID: 27355625 PMCID: PMC4927098 DOI: 10.1371/journal.pone.0156807] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
Abstract
Chronic airway infection is a hallmark feature of cystic fibrosis (CF) disease. In the present study, sputum samples from CF patients were collected and characterized by 16S rRNA gene-targeted approach, to assess how lung microbiota composition changes following a severe decline in lung function. In particular, we compared the airway microbiota of two groups of patients with CF, i.e. patients with a substantial decline in their lung function (SD) and patients with a stable lung function (S). The two groups showed a different bacterial composition, with SD patients reporting a more heterogeneous community than the S ones. Pseudomonas was the dominant genus in both S and SD patients followed by Staphylococcus and Prevotella. Other than the classical CF pathogens and the most commonly identified non-classical genera in CF, we found the presence of the unusual anaerobic genus Sneathia. Moreover, the oligotyping analysis revealed the presence of other minor genera described in CF, highlighting the polymicrobial nature of CF infection. Finally, the analysis of correlation and anti-correlation networks showed the presence of antagonism and ecological independence between members of Pseudomonas genus and the rest of CF airways microbiota, with S patients showing a more interconnected community in S patients than in SD ones. This population structure suggests a higher resilience of S microbiota with respect to SD, which in turn may hinder the potential adverse impact of aggressive pathogens (e.g. Pseudomonas). In conclusion, our findings shed a new light on CF airway microbiota ecology, improving current knowledge about its composition and polymicrobial interactions in patients with CF.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, Florence, Italy
| | - Patrizia Paganin
- Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Loredana Lopez
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy
| | - Chiara Vanni
- Department of Biology, University of Florence, Florence, Italy
| | - Claudia Dalmastri
- Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Cristina Cantale
- Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Loretta Daddiego
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy
| | - Gaetano Perrotta
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy
| | - Daniela Dolce
- Department of Pediatrics, Cystic Fibrosis Center, Meyer Hospital, Florence, Italy
| | - Patrizia Morelli
- Department of Pediatrics, Cystic Fibrosis Center, G. Gaslini Institute, Genoa, Italy
| | - Vanessa Tuccio
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | | | - Ersilia Vita Fiscarelli
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | - Giovanni Taccetti
- Department of Pediatrics, Cystic Fibrosis Center, Meyer Hospital, Florence, Italy
| | - Vincenzina Lucidi
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
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Hedin C, van der Gast CJ, Rogers GB, Cuthbertson L, McCartney S, Stagg AJ, Lindsay JO, Whelan K. Siblings of patients with Crohn's disease exhibit a biologically relevant dysbiosis in mucosal microbial metacommunities. Gut 2016; 65:944-53. [PMID: 25856344 DOI: 10.1136/gutjnl-2014-308896] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/11/2015] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To determine the existence of mucosal dysbiosis in siblings of patients with Crohn's disease (CD) using 454 pyrosequencing and to comprehensively characterise and determine the influence of genotypical and phenotypical factors, on that dysbiosis. Siblings of patients with CD have elevated risk of developing CD and display aspects of disease phenotype, including faecal dysbiosis. Whether the mucosal microbiota is disrupted in these at-risk individuals is unknown. DESIGN Rectal biopsy DNA was extracted from 21 patients with quiescent CD, 17 of their healthy siblings and 19 unrelated healthy controls. Mucosal microbiota was analysed by 16S rRNA gene pyrosequencing and were classified into core and rare species. Genotypical risk was determined using Illumina Immuno BeadChip, faecal calprotectin by ELISA and blood T-cell phenotype by flow cytometry. RESULTS Core microbiota of both patients with CD and healthy siblings was significantly less diverse than controls. Metacommunity profiling (Bray-Curtis (SBC) index) showed the sibling core microbial composition to be more similar to CD (SBC=0.70) than to healthy controls, whereas the sibling rare microbiota was more similar to healthy controls (SBC=0.42). Faecalibacterium prausnitzii contributed most to core metacommunity dissimilarity both between siblings and controls, and between patients and controls. Phenotype/genotype markers of CD risk significantly influenced microbiota variation between and within groups, of which genotype had the largest effect. CONCLUSIONS Individuals with elevated CD-risk display mucosal dysbiosis characterised by reduced diversity of core microbiota and lower abundance of F. prausnitzii. This dysbiosis in healthy people at risk of CD implicates microbiological processes in CD pathogenesis.
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Affiliation(s)
- Charlotte Hedin
- Faculty of Life Sciences & Medicine, Diabetes and Nutritional Sciences Division, King's College London, London, UK Centre for Immunology and Infectious Disease, Blizard Institute, Queen Mary University of London, London, UK
| | | | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Infection and Immunity Theme, Flinders University, Adelaide, Australia
| | - Leah Cuthbertson
- NERC Centre for Ecology & Hydrology, Wallingford, Oxfordshire, UK
| | - Sara McCartney
- Centre for Gastroenterology and Nutrition, University College London, London, UK
| | - Andrew J Stagg
- Centre for Immunology and Infectious Disease, Blizard Institute, Queen Mary University of London, London, UK
| | - James O Lindsay
- Centre for Digestive Diseases, Blizard Institute, Queen Mary University of London, London, UK Department of Gastroenterology, Barts Health NHS Trust, London, UK
| | - Kevin Whelan
- Faculty of Life Sciences & Medicine, Diabetes and Nutritional Sciences Division, King's College London, London, UK
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43
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Shifts of live bacterial community in secondary effluent by chlorine disinfection revealed by Miseq high-throughput sequencing combined with propidium monoazide treatment. Appl Microbiol Biotechnol 2016; 100:6435-6446. [DOI: 10.1007/s00253-016-7452-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/01/2016] [Accepted: 03/05/2016] [Indexed: 10/22/2022]
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Habtewold T, Duchateau L, Christophides GK. Flow cytometry analysis of the microbiota associated with the midguts of vector mosquitoes. Parasit Vectors 2016; 9:167. [PMID: 27004717 PMCID: PMC4802834 DOI: 10.1186/s13071-016-1438-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/08/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The scientific interest to understand the function and structure of the microbiota associated with the midgut of mosquito disease vectors is increasing. The advancement of such a knowledge has encountered challenges and limitations associated with conventional culture-based and PCR techniques. METHODS Flow cytometry (FCM) combined with various cell marking dyes have been successfully applied in the field of ecological microbiology to circumvent the above shortcomings. Here, we describe FCM technique coupled with live/dead differential staining dyes SYBR Green I (SGI) and Propidium Iodide (PI) to quantify and study other essential characteristics of the mosquito gut microbiota. RESULTS A clear discrimination between cells and debris, as well as between live and dead cells was achieved when the midgut homogenate was subjected to staining with 5 × 103 dilution of the SGI and 30 μM concentration of the PI. Reproducibly, FCM event collections produced discrete populations including non-fluorescent cells, SYBR positive cells, PI fluorescing cells and cells that fluoresce both in SYBR and PI, all these cell populations representing, respectively, background noise, live bacterial, dead cells and inactive cells with partial permeability to PI. The FCM produced a strong linear relationship between cell counts and their corresponding dilution factors (R (2) = 0.987), and the technique has a better precision compared to qRT-PCR. The FCM count of the microbiota reached a peak load at 18 h post-feeding and started declining at 24 h. The present FCM technique also successfully applied to quantify bacterial cells in fixed midgut samples that were homogenized in 4 % PFA. CONCLUSION The FCM technique described here offers enormous potential and possibilities of integration with advanced molecular biochemical techniques for the study of the microbiota community in disease vector mosquitoes.
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Affiliation(s)
- Tibebu Habtewold
- Department of Life Sciences, Imperial College London, London, UK ,Department of Comparative Physiology and Biometrics, University of Ghent, Ghent, Belgium
| | - Luc Duchateau
- Department of Comparative Physiology and Biometrics, University of Ghent, Ghent, Belgium
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Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention. ISME JOURNAL 2015; 10:1081-91. [PMID: 26555248 PMCID: PMC4820042 DOI: 10.1038/ismej.2015.198] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/22/2015] [Indexed: 01/24/2023]
Abstract
Pulmonary symptoms in cystic fibrosis (CF) begin in early life with chronic lung infections and concomitant airway inflammation leading to progressive loss of lung function. Gradual pulmonary function decline is interspersed with periods of acute worsening of respiratory symptoms known as CF pulmonary exacerbations (CFPEs). Cumulatively, CFPEs are associated with more rapid disease progression. In this study multiple sputum samples were collected from adult CF patients over the course of CFPEs to better understand how changes in microbiota are associated with CFPE onset and management. Data were divided into five clinical periods: pre-CFPE baseline, CFPE, antibiotic treatment, recovery, and post-CFPE baseline. Samples were treated with propidium monoazide prior to DNA extraction, to remove the impact of bacterial cell death artefacts following antibiotic treatment, and then characterised by 16S rRNA gene-targeted high-throughput sequencing. Partitioning CF microbiota into core and rare groups revealed compositional resistance to CFPE and resilience to antibiotics interventions. Mixed effects modelling of core microbiota members revealed no significant negative impact on the relative abundance of Pseudomonas aeruginosa across the exacerbation cycle. Our findings have implications for current CFPE management strategies, supporting reassessment of existing antimicrobial treatment regimens, as antimicrobial resistance by pathogens and other members of the microbiota may be significant contributing factors.
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46
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Caverly LJ, Zhao J, LiPuma JJ. Cystic fibrosis lung microbiome: opportunities to reconsider management of airway infection. Pediatr Pulmonol 2015; 50 Suppl 40:S31-8. [PMID: 26335953 DOI: 10.1002/ppul.23243] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/09/2015] [Accepted: 06/16/2015] [Indexed: 11/06/2022]
Abstract
The importance of infection in the pathogenesis of cystic fibrosis (CF) lung disease has been long recognized, and the use of antibiotics targeting bacteria identified in cultures of respiratory specimens has played a critical role in improving outcomes for individuals with CF. Over the past ∼15 years, the use of culture-independent methods to assess airway microbiology in CF has revealed complex and dynamic CF airway bacterial communities. Recent areas of investigation of the CF lung microbiome have included exploring how bacterial community structures change over time, particularly with respect to disease progression or pulmonary exacerbation, and in response to antibiotic therapies. This review will discuss what has been learned from these studies as well as how these findings offer opportunities to further refine management of CF airway infection.
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Affiliation(s)
- Lindsay J Caverly
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jiangchao Zhao
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan
| | - John J LiPuma
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan
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47
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Habtewold T, Groom Z, Duchateau L, Christophides GK. Detection of viable plasmodium ookinetes in the midguts of anopheles coluzzi using PMA-qrtPCR. Parasit Vectors 2015; 8:455. [PMID: 26373633 PMCID: PMC4572643 DOI: 10.1186/s13071-015-1087-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/11/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Mosquito infection with malaria parasites depends on complex interactions between the mosquito immune response, the parasite developmental program and the midgut microbiota. Simultaneous monitoring of the parasite and bacterial dynamics is important when studying these interactions. PCR based methods of genomic DNA (gDNA) have been widely used, but their inability to discriminate between live and dead cells compromises their application. The alternative method of quantification of mRNA mainly reports on cell activity rather than density. METHOD Quantitative real-time (qrt) PCR in combination with Propidium Monoazide (PMA) treatment (PMA-qrtPCR) has been previously used for selectively enumerating viable microbial cells. PMA penetrates damaged cell membranes and intercalates in the DNA inhibiting its PCR amplification. Here, we tested the potential of PMA-qrtPCR to discriminate between and quantify live and dead Plasmodium berghei malarial parasites and commensal bacteria in the midgut of Anopheles coluzzii Coetzee & Wilkerson 2013 (formerly An. gambiae M-form). RESULTS By combining microscopic observations with reverse transcriptase PCR (RT-PCR) we reveal that, in addition to gDNA, mRNA from dead parasites also persists inside the mosquito midgut, therefore its quantification cannot accurately reflect live-only parasites at the time of monitoring. In contrast, pre-treating the samples with PMA selectively inhibited qrtPCR amplification of parasite gDNA, with about 15 cycles (Ct-value) difference between PMA-treated and control samples. The limit of detection corresponds to 10 Plasmodium ookinetes. Finally, we show that the PMA-qrtPCR method can be used to quantify bacteria that are present in the mosquito midgut. CONCLUSION The PMA-qrtPCR is a suitable method for quantification of viable parasites and bacteria in the midgut of Anopheles mosquitoes. The method will be valuable when studying the molecular interactions between the mosquito, the malaria parasite and midgut microbiota.
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Affiliation(s)
- Tibebu Habtewold
- Department of Life Sciences, Imperial College London, London, UK.
- Department of Comparative Physiology and Biometrics, University of Ghent, Ghent, Belgium.
| | - Zoe Groom
- Department of Life Sciences, Imperial College London, London, UK
- Costello Medical Consulting, Cambridge, UK
| | - Luc Duchateau
- Department of Comparative Physiology and Biometrics, University of Ghent, Ghent, Belgium
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48
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Newbold LK, Oliver AE, Cuthbertson L, Walkington SE, Gweon HS, Heard MS, van der Gast CJ. Rearing and foraging affects bumblebee (Bombus terrestris) gut microbiota. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:634-41. [PMID: 25994560 DOI: 10.1111/1758-2229.12299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/12/2015] [Indexed: 05/14/2023]
Abstract
Bumblebees are ecologically and economically important as pollinators of crop and wild plants, especially in temperate systems. Species, such as the buff-tailed bumblebee (Bombus terrestris), are reared commercially to pollinate high-value crops. Their highly specific gut microbiota, characterized by low diversity, may affect nutrition and immunity and are likely to be important for fitness and colony health. However, little is known about how environmental factors affect bacterial community structure. We analysed the gut microbiota from three groups of worker bumblebees (B. terrestris) from distinct colonies that varied in rearing and foraging characteristics: commercially reared with restricted foraging (RR); commercially reared with outside foraging (RF); and wild-caught workers (W). Contrary to previous studies, which indicate that bacterial communities are highly conserved across workers, we found that RF individuals had an intermediate community structure compared with RR and W types. Further, this was shaped by differences in the abundances of common operational taxonomic units (OTUs) and the diversity of rare OTUs present, which we propose results from an increase in the variety of carbohydrates obtained through foraging.
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Affiliation(s)
| | - Anna E Oliver
- NERC Centre for Ecology & Hydrology, Wallingford, OX10 8BB, UK
| | | | | | - Hyun S Gweon
- NERC Centre for Ecology & Hydrology, Wallingford, OX10 8BB, UK
| | - Matthew S Heard
- NERC Centre for Ecology & Hydrology, Wallingford, OX10 8BB, UK
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Aho VTE, Pereira PAB, Haahtela T, Pawankar R, Auvinen P, Koskinen K. The microbiome of the human lower airways: a next generation sequencing perspective. World Allergy Organ J 2015; 8:23. [PMID: 26140078 PMCID: PMC4468963 DOI: 10.1186/s40413-015-0074-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 06/01/2015] [Indexed: 12/22/2022] Open
Abstract
For a long time, the human lower airways were considered a sterile environment where the presence of microorganisms, typically revealed by culturing, was interpreted as an abnormal health state. More recently, high-throughput sequencing-based studies have led to a shift in this perception towards the notion that even in healthy conditions the lower airways show either transient presence or even permanent colonization by microorganisms. However, challenges related to low biomass and contamination in samples still remain, and the composition, structure and dynamics of such putative microbial communities are unclear. Here, we review the evidence for the presence of microbial communities in the human lower airways, in healthy subjects and within the context of medical conditions of interest. We also provide an overview of the methodology pertinent to high-throughput sequencing studies, specifically those based on amplicon sequencing, including a discussion of good practices and common pitfalls.
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Affiliation(s)
- Velma T. E. Aho
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland
| | - Pedro A. B. Pereira
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Ruby Pawankar
- Division of Allergy, Department of Pediatrics, Nippon Medical School, Tokyo, Japan
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland
| | - Kaisa Koskinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P.O. Box 56 (Viikinkaari 4), 00014 Helsinki, Finland
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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50
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Directly sampling the lung of a young child with cystic fibrosis reveals diverse microbiota. Ann Am Thorac Soc 2015; 11:1049-55. [PMID: 25072206 DOI: 10.1513/annalsats.201311-383oc] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
RATIONALE The airways of people with cystic fibrosis (CF) are chronically infected with a variety of bacterial species. Although routine culture methods are usually used to diagnose these infections, culture-independent, DNA-based methods have identified many bacterial species in CF respiratory secretions that are not routinely cultured. Many prior culture-independent studies focused either on microbiota in explanted CF lungs, reflecting end-stage disease, or those in oropharyngeal swabs, which likely sample areas in addition to the lower airways. Therefore, it was unknown whether the lower airways of children with CF, well before end-stage but with symptomatic lung disease, truly contained diverse microbiota. OBJECTIVES To define the microbiota in the diseased lung tissue of a child who underwent lobectomy for severe, localized CF lung disease. METHODS After pathologic examination verified that this child's lung tissue reflected CF lung disease, we used bacterial ribosomal RNA gene pyrosequencing and computational phylogenetic analysis to identify the microbiota in serial sections of the tissue. MEASUREMENTS AND MAIN RESULTS This analysis identified diverse, and anatomically heterogeneous, bacterial populations in the lung tissue that contained both culturable and nonculturable species, including abundant Haemophilus, Ralstonia, and Propionibacterium species. Routine clinical cultures identified only Staphylococcus aureus, which represented only a small fraction of the microbiota found by sequencing. Microbiota analysis of an intraoperative oropharyngeal swab identified predominantly Streptococcus species. The oropharyngeal findings therefore represented the lung tissue microbiota poorly, in agreement with findings from earlier studies of oropharyngeal swabs in end-stage disease. CONCLUSIONS These results support the concept that diverse and spatially heterogeneous microbiota, not necessarily dominated by "traditional CF pathogens," are present in the airways of young, symptomatic children with early CF lung disease.
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