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Hauser S, Lazarevic V, Tournoud M, Ruppé E, Santiago Allexant E, Guigon G, Schicklin S, Lanet V, Girard M, Mirande C, Gervasi G, Schrenzel J. A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia. Microbiol Spectr 2023; 11:e0129423. [PMID: 37889000 PMCID: PMC10715005 DOI: 10.1128/spectrum.01294-23] [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: 05/09/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE The management of ventilator-associated pneumonia and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen. To this end, we propose a metagenomic sequencing assay that includes the use of an internal sample processing control for the quantitative detection of 20 relevant bacterial species from bronchoalveolar lavage samples.
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Affiliation(s)
| | - V. Lazarevic
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | - E. Ruppé
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | | | | | - V. Lanet
- bioMérieux, Marcy-l'Étoile, France
| | - M. Girard
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - C. Mirande
- bioMérieux, La Balme-les-Grottes, France
| | | | - J. Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
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2
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Abstract
Cancer cells originate from a series of acquired genetic mutations that can drive their uncontrolled cell proliferation and immune evasion. Environmental factors, including the microorganisms that colonize the human body, can shift the metabolism, growth pattern and function of neoplastic cells and shape the tumour microenvironment. Dysbiosis of the gut microbiome is now recognized as a hallmark of cancer by the scientific community. However, only a few microorganisms have been identified that directly initiate tumorigenesis or skew the immune system to generate a tumour-permissive milieu. Over the past two decades, research on the human microbiome and its functionalities within and across individuals has revealed microbiota-focused strategies for health and disease. Here, we review the evolving understanding of the mechanisms by which the microbiota acts in cancer initiation, promotion and progression. We explore the roles of bacteria in gastrointestinal tract malignancies and cancers of the lung, breast and prostate. Finally, we discuss the promises and limitations of targeting or harnessing bacteria in personalized cancer prevention, diagnostics and treatment.
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Affiliation(s)
- Geniver El Tekle
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Harvard T. H. Chan Microbiome in Public Health Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- The Harvard T. H. Chan Microbiome in Public Health Center, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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3
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Amar Y, Lagkouvardos I, Silva RL, Ishola OA, Foesel BU, Kublik S, Schöler A, Niedermeier S, Bleuel R, Zink A, Neuhaus K, Schloter M, Biedermann T, Köberle M. Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA. MICROBIOME 2021; 9:123. [PMID: 34039428 PMCID: PMC8157445 DOI: 10.1186/s40168-021-01067-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/01/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities. RESULTS We investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 105 CFU and that Benzonase digest is not sufficient to overcome this bias. CONCLUSIONS The BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. Video abstract.
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Affiliation(s)
- Yacine Amar
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Ilias Lagkouvardos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), HCMR, Heraklion, Greece
- Core Facility Microbiome, Technische Universität München, 85354, Freising, Germany
| | - Rafaela L Silva
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Oluwaseun Ayodeji Ishola
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Bärbel U Foesel
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
- DKFZ German Cancer Research Center, Berlin, Germany
| | - Sebastian Niedermeier
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Rachela Bleuel
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Alexander Zink
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, Technische Universität München, 85354, Freising, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, 85354, Freising, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, 85354, Freising, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany.
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany.
| | - Martin Köberle
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
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Ramírez-Labrada AG, Isla D, Artal A, Arias M, Rezusta A, Pardo J, Gálvez EM. The Influence of Lung Microbiota on Lung Carcinogenesis, Immunity, and Immunotherapy. Trends Cancer 2020; 6:86-97. [PMID: 32061309 DOI: 10.1016/j.trecan.2019.12.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022]
Abstract
Microbiota have emerged as key modulators of both the carcinogenic process and the immune response against cancer cells, and, thus, it seems to influence the efficacy of immunotherapy. While most studies have focused on analyzing the influence of gut microbiota, its composition substantially differs from that in the lung. Here, we describe how microbial life in the lungs is associated with host immune status in the lungs and, thus, how the identification of the microbial populations in the lower respiratory tract rather than in the gut might be key to understanding the lung carcinogenic process and to predict the efficacy of different treatments. Understanding the influence of lung microbiota on host immunity may identify new therapeutic targets and help to design new immunotherapy approaches to treat lung cancer.
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Affiliation(s)
- Ariel G Ramírez-Labrada
- Unidad de Nanotoxicología e Inmunotoxicología (UNATI), Instituto de Investigación Sanitaria Aragón (IIS Aragón), Centro de Investigación Biomédica de Aragón (CIBA), Zaragoza, Spain
| | - Dolores Isla
- Medical Oncology Department, Instituto de Investigación Sanitaria Aragón, Hospital Clinico Universitario Lozano Blesa, Zaragoza, Spain
| | - Angel Artal
- Medical Oncology Department, Instituto de Investigación Sanitaria Aragón (IIS Aragón), Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Maykel Arias
- Instituto de Carboquímica ICB-CSIC, Zaragoza, Spain
| | - Antonio Rezusta
- Department of Microbiology, Hospital Universitario Miguel Servet, Zaragoza, Spain; Department of Microbiology, Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, Spain
| | - Julián Pardo
- Department of Microbiology, Preventive Medicine and Public Health, University of Zaragoza, Zaragoza, Spain; Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain; Aragón I + D Foundation (ARAID), Government of Aragon, Zaragoza, Spain
| | - Eva M Gálvez
- Instituto de Carboquímica ICB-CSIC, Zaragoza, Spain.
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5
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Cho DY, Hunter RC, Ramakrishnan VR. The Microbiome and Chronic Rhinosinusitis. Immunol Allergy Clin North Am 2020; 40:251-263. [PMID: 32278449 DOI: 10.1016/j.iac.2019.12.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chronic rhinosinusitis (CRS) is persistent inflammation and/or infection of the nasal cavity and paranasal sinuses. Recent advancements in culture-independent molecular techniques have enhanced understanding of interactions between sinus microbiota and upper airway microenvironment. The dysbiosis hypothesis-alteration of microbiota associated with perturbation of the local ecological landscape-is suggested as a mechanism involved in CRS pathogenesis. This review discusses the complex role of the microbiota in health and in CRS and considerations in sinus microbiome investigation, dysbiosis of sinus microbiota in CRS, microbial interactions in CRS, and development of preclinical models. The authors conclude with future directions for CRS-associated microbiome research.
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Affiliation(s)
- Do-Yeon Cho
- Department of Otolaryngology-Head & Neck Surgery, University of Alabama at Birmingham, 1155 Faculty Office Tower, 510 20th Street South, Birmingham, AL 35233, USA; Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ryan C Hunter
- Department of Microbiology & Immunology, University of Minnesota, 3-115 Microbiology Research Facility, 689 23rd Avenue SE, Minneapolis, MN 55455, USA
| | - Vijay R Ramakrishnan
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado, 12631 East 17th Avenue, B205, Aurora, CO 80045, USA.
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Kim AS, Willis AL, Laubitz D, Sharma S, Song BH, Chiu AG, Le CH, Chang EH. The effect of maxillary sinus antrostomy size on the sinus microbiome. Int Forum Allergy Rhinol 2018; 9:30-38. [PMID: 30358937 DOI: 10.1002/alr.22224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/17/2018] [Accepted: 09/10/2018] [Indexed: 11/08/2022]
Abstract
BACKGROUND The optimal maxillary antrostomy size to surgically treat sinusitis is not well known. In this study, we examined clinical metrics of disease severity and symptom scores, measured secreted inflammatory markers, and characterized the sinus microbiome to determine if there were significant differences in outcome between different maxillary ostial sizes. METHODS Prospective randomized, single-blinded clinical trial enrolling 12 individuals diagnosed with recurrent acute or chronic rhinosinusitis. Each patient was blinded and randomized to receive minimal maxillary ostial dilation via balloon sinuplasty on 1 side vs a mega-antrostomy on the contralateral side. Data collected included symptom scores (20-item Sino-Nasal Outcome Test [SNOT-20]), endoscopy, and radiologic Lund-Mackay scores. During surgery and at their postoperative visit swabs were obtained from each maxillary sinus, and 16S DNA and inflammatory cytokine levels analyzed. The use of each patient as their own control allowed us to minimize confounding variables. RESULTS There was statistically significant improvement in SNOT-20 symptom scores postoperatively in all patients. There were no significant differences between maxillary ostial size in postoperative endoscopy scores, cytokine profile, or bacterial burden. There were statistically significant differences in relative postoperative abundance of Staphylococcus, Lactococcus, and Cyanobacteria between the mega-antrostomy and mini-antrostomy. CONCLUSIONS The method used in surgical maxillary antrostomies had no effect on endoscopy scores or cytokine profiles. Microbiome analysis determined significant differences between the different antrostomy sizes in postoperative Staphylococcus, Lactococcus, and Cyanobacteria abundance. The clinical significance of these changes in the sinus microbiome are not known but may be a result of increased access to postoperative sinonasal irrigations.
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Affiliation(s)
- Alexander S Kim
- Department of Otolaryngology-Head and Neck Surgery, University of Arizona College of Medicine, Tucson, AZ
| | - Amanda L Willis
- Department of Otolaryngology-Head and Neck Surgery, University of Arizona College of Medicine, Tucson, AZ
| | - Daniel Laubitz
- Department of Pediatrics, University of Arizona College of Medicine, Tucson, AZ
| | - Saurabh Sharma
- Department of Otolaryngology-Head and Neck Surgery, University of Arizona College of Medicine, Tucson, AZ
| | - Brian H Song
- Department of Otolaryngology-Head and Neck Surgery, University of Arizona College of Medicine, Tucson, AZ
| | - Alexander G Chiu
- Department of Otolaryngology-Head and Neck Surgery, University of Kansas Medical Center, Kansas City, KS
| | - Christopher H Le
- Department of Otolaryngology-Head and Neck Surgery, University of Arizona College of Medicine, Tucson, AZ
| | - Eugene H Chang
- Department of Otolaryngology-Head and Neck Surgery, University of Arizona College of Medicine, Tucson, AZ
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7
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Liu Y, Wong KKW, Ko EYL, Chen X, Huang J, Tsui SKW, Li TC, Chim SSC. Systematic Comparison of Bacterial Colonization of Endometrial Tissue and Fluid Samples in Recurrent Miscarriage Patients: Implications for Future Endometrial Microbiome Studies. Clin Chem 2018; 64:1743-1752. [PMID: 30237148 DOI: 10.1373/clinchem.2018.289306] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/23/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND A recent study has reported that the microbiota in endometrial fluid of patients receiving in vitro fertilization and embryo transfer (IVF-ET) may predict implantation and pregnancy rates. However, studies are lacking that simultaneously compare the microbiota between endometrial fluid and tissue samples. Whether the microbiota composition in endometrial fluid reflects that in the endometrial tissue remains unclear. METHODS We systematically profiled the microbiota in endometrial fluid and tissue samples of IVF-ET patients using massively parallel sequencing. The bacterial 16S ribosomal RNA gene (V4 region) was PCR-amplified. Sequencing reads with >98% nucleotide identity were clustered as a bacterial taxon. To account for the different number of reads per sample, we normalized the read counts of each taxon before comparing its relative abundances across samples. RESULTS Thirteen taxa, including Verrucomicrobiaceae, Brevundimonas, Achromobacter, Exiguobacterium, and Flavobacterium, were consistently detected only in endometrial tissue samples but not fluid samples. Eight taxa were detected in fluid but not tissue. Twenty-two taxa were differentially abundant between fluid and tissue samples (adjusted P values, 4.1 × 10-25 to 0.025). The numbers of taxa identified per 1000 sequencing reads, diversity, and evenness in fluid samples were smaller than those in tissue samples. CONCLUSIONS Our data suggest that the microbiota composition in endometrial fluid does not fully reflect that in endometrial tissue. Sampling from both endometrial fluid and biopsy allows a more comprehensive view of microbial colonization. Further efforts are needed to identify the preanalytical effects, including sampling sites, methods, and sequencing depth, on profiling endometrial microbiota.
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Affiliation(s)
- Yingyu Liu
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Karen Ka-Wing Wong
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Elaine Yee-Ling Ko
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Xiaoyan Chen
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Jin Huang
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Tin Chiu Li
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Stephen Siu-Chung Chim
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China;
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8
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Jain R, Hoggard M, Zoing M, Jiang Y, Biswas K, Taylor MW, Douglas RG. The effect of medical treatments on the bacterial microbiome in patients with chronic rhinosinusitis: a pilot study. Int Forum Allergy Rhinol 2018; 8:890-899. [PMID: 29517178 DOI: 10.1002/alr.22110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 01/16/2018] [Accepted: 02/01/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Antibiotics and corticosteroids are prescribed to patients with chronic rhinosinusitis (CRS) to reduce bacterial burden and mucosal inflammation. Unfortunately, clinical improvement is often short-lived and symptoms frequently recur following cessation of treatment. The impact of these systemic therapies on bacterial communities is not well understood. Improved knowledge of how medical therapies influence the intranasal ecosystem may allow for more effective prescribing and the development of more targeted treatments. METHODS Twenty patients with CRS were randomized to receive either doxycycline 100 mg twice daily or prednisone 30 mg once daily for 7 days. A further 6 patients with CRS were recruited as untreated controls. Swabs were taken immediately before and after the study period. Symptom scores (22-item Sino-Nasal Outcome Test [SNOT-22]) were recorded. Bacterial communities were characterized using 16S ribosomal RNA (rRNA) gene-targeted amplicon sequencing. Bacterial abundance was estimated using quantitative polymerase chain reaction (PCR) of 16S rRNA gene copies. RESULTS Bacterial profiles were dominated by members of the genera Corynebacterium and Staphylococcus. Patients treated with either doxycycline or prednisone had variable and unpredictable changes in communities. The average relative abundance of Propionibacterium increased after treatment in the doxycycline treatment group, and Corynebacterium reduced in the prednisone group. Significant differences in clinical scores, bacterial community richness, diversity, and bacterial abundance were not seen after treatment. CONCLUSION The short-term response of bacterial communities to antibiotic or corticosteroid therapy is unpredictable. This study suggests that the use of systemic therapy in patients with stable CRS should be rationalized to minimize antibiotic-associated morbidity and bacterial dysbiosis.
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Affiliation(s)
- Ravi Jain
- Department of Surgery, The University of Auckland, Auckland, New Zealand
| | - Michael Hoggard
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Melissa Zoing
- Department of Surgery, The University of Auckland, Auckland, New Zealand
| | - Yannan Jiang
- Department of Statistics, The University of Auckland, Auckland, New Zealand
| | - Kristi Biswas
- Department of Surgery, The University of Auckland, Auckland, New Zealand
| | - Michael W Taylor
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Richard G Douglas
- Department of Surgery, The University of Auckland, Auckland, New Zealand
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Copeland E, Leonard K, Carney R, Kong J, Forer M, Naidoo Y, Oliver BGG, Seymour JR, Woodcock S, Burke CM, Stow NW. Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites. Front Cell Infect Microbiol 2018. [PMID: 29541629 PMCID: PMC5836553 DOI: 10.3389/fcimb.2018.00057] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is an inflammatory condition that affects up to 12% of the human population in developed countries. Previous studies examining the potential role of the sinus bacterial microbiota within CRS infections have found inconsistent results, possibly because of inconsistencies in sampling strategies. The aim of this study was to determine whether the sinus microbiome is altered in CRS and additionally if the middle meatus is a suitable representative site for sampling the sinus microbiome. Swab samples were collected from 12 healthy controls and 21 CRS patients, including all eight sinuses for CRS patients and between one and five sinuses for control subjects. The left and right middle meatus and nostril swabs were also collected. Significant differences in the sinus microbiomes between CRS and control samples were revealed using high-throughput 16S rRNA gene sequencing. The genus Escherichia was over-represented in CRS sinuses, and associations between control patients and Corynebacterium and Dolosigranulum were also identified. Comparisons of the middle meatuses between groups did not reflect these differences, and the abundance of the genus Escherichia was significantly lower at this location. Additionally, intra-patient variation was lower between sinuses than between sinus and middle meatus, which together with the above results suggests that the middle meatus is not an effective representative sampling site.
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Affiliation(s)
- Elizabeth Copeland
- The School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Katherine Leonard
- Sydney Centre for Ear Nose and Throat, Frenchs Forest, Sydney, NSW, Australia
| | - Richard Carney
- The Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Justin Kong
- Department of Otorhinolaryngology, Royal North Shore Hospital, University of Sydney, Sydney, NSW, Australia
| | - Martin Forer
- Department of Otorhinolaryngology, Royal North Shore Hospital, University of Sydney, Sydney, NSW, Australia
| | - Yuresh Naidoo
- Department of Otorhinolaryngology, Concord Hospital, University of Sydney, Sydney, NSW, Australia
| | - Brian G G Oliver
- The School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia.,Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Justin R Seymour
- The Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Stephen Woodcock
- The Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Catherine M Burke
- The School of Life Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Nicholas W Stow
- Department of Otorhinolaryngology, Royal North Shore Hospital, University of Sydney, Sydney, NSW, Australia.,Woolcock Institute of Medical Research, The University of Sydney, Sydney, NSW, Australia
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10
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Chronic Rhinosinusitis and the Evolving Understanding of Microbial Ecology in Chronic Inflammatory Mucosal Disease. Clin Microbiol Rev 2017; 30:321-348. [PMID: 27903594 DOI: 10.1128/cmr.00060-16] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Chronic rhinosinusitis (CRS) encompasses a heterogeneous group of debilitating chronic inflammatory sinonasal diseases. Despite considerable research, the etiology of CRS remains poorly understood, and debate on potential roles of microbial communities is unresolved. Modern culture-independent (molecular) techniques have vastly improved our understanding of the microbiology of the human body. Recent studies that better capture the full complexity of the microbial communities associated with CRS reintroduce the possible importance of the microbiota either as a direct driver of disease or as being potentially involved in its exacerbation. This review presents a comprehensive discussion of the current understanding of bacterial, fungal, and viral associations with CRS, with a specific focus on the transition to the new perspective offered in recent years by modern technology in microbiological research. Clinical implications of this new perspective, including the role of antimicrobials, are discussed in depth. While principally framed within the context of CRS, this discussion also provides an analogue for reframing our understanding of many similarly complex and poorly understood chronic inflammatory diseases for which roles of microbes have been suggested but specific mechanisms of disease remain unclear. Finally, further technological advancements on the horizon, and current pressing questions for CRS microbiological research, are considered.
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11
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Scheiermann J, Klinman DM. Three distinct pneumotypes characterize the microbiome of the lung in BALB/cJ mice. PLoS One 2017; 12:e0180561. [PMID: 28683098 PMCID: PMC5500332 DOI: 10.1371/journal.pone.0180561] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 06/16/2017] [Indexed: 01/05/2023] Open
Abstract
Bacteria can rarely be isolated from normal healthy lungs using conventional culture techniques, supporting the traditional belief that the lungs are sterile. Yet recent studies using next generation sequencing report that bacterial DNA commonly found in the upper respiratory tract (URT) is present at lower levels in the lungs. Interpretation of that finding is complicated by the technical limitations and potential for contamination introduced when dealing with low biomass samples. The current work sought to overcome those limitations to clarify the number, type and source of bacteria present in the lungs of normal mice. Results showed that the oral microbiome is diverse and highly conserved whereas murine lung samples fall into three distinct patterns. 33% of the samples were sterile, as they lacked culturable bacteria and their bacterial DNA content did not differ from background. 9% of samples contained comparatively higher amounts of bacterial DNA whose composition mimicked that detected in the URT. A final group (58%) contained smaller amounts of microbial DNA whose composition was correlating to that of rodent chow and cage bedding, likely acquired by inspiration of food and bedding fragments. By analyzing each sample independently rather than working with group averages, this work eliminated the bias introduced by aspiration-contaminated samples to establish that three distinct microbiome pneumotypes are present in normal murine lungs.
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Affiliation(s)
- Julia Scheiermann
- Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Dennis M. Klinman
- Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
- * E-mail:
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12
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Shankar J. Insights into study design and statistical analyses in translational microbiome studies. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:249. [PMID: 28706917 DOI: 10.21037/atm.2017.01.13] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Research questions in translational microbiome studies are substantially more complex than their counterparts in basic science. Robust study designs with appropriate statistical analysis frameworks are pivotal to the success of these translational studies. This review considers how study designs can account for heterogeneous phenotypes by adopting representative sampling schemes for recruiting the study population and making careful choices about the control population. Advantages and limitations of 16S profiling and whole-genome sequencing, the two primary techniques for measuring the microbiome, are discussed followed by an overview of bioinformatic processing of high-throughput sequencing data from these measurements. Practical insights into the downstream statistical analyses including data processing and integration, variable transformations, and data exploration are provided. The merits of regularization and ensemble modeling for analyzing microbiome data are discussed along with a recommendation for selecting modeling approaches based on data-driven simulations and objective evaluation. The review builds on several recent discussions of study design issues in microbiome research but with a stronger emphasis on the downstream and often-ignored aspects of statistical analyses that are crucial for bridging the gap between basic science and translation.
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Lal D, Keim P, Delisle J, Barker B, Rank MA, Chia N, Schupp JM, Gillece JD, Cope EK. Mapping and comparing bacterial microbiota in the sinonasal cavity of healthy, allergic rhinitis, and chronic rhinosinusitis subjects. Int Forum Allergy Rhinol 2017; 7:561-569. [PMID: 28481057 DOI: 10.1002/alr.21934] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 02/04/2017] [Accepted: 02/14/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND The role of microbiota in sinonasal inflammation can be further understood by targeted sampling of healthy and diseased subjects. We compared the microbiota of the middle meatus (MM) and inferior meatus (IM) in healthy, allergic rhinitis (AR), and chronic rhinosinusitis (CRS) subjects to characterize intrasubject, intersubject, and intergroup differences. METHODS Subjects were recruited in the office, and characterized into healthy, AR, and CRS groups. Endoscopically-guided swab samples were obtained from the MM and IM bilaterally. Bacterial microbiota were characterized by sequencing the V3-V4 region of the 16S ribosomal RNA (rRNA) gene. RESULTS Intersubject microbiome analyses were conducted in 65 subjects: 8 healthy, 11 AR, and 46 CRS (25 CRS with nasal polyps [CRSwNP]; 21 CRS without nasal polyps [CRSsNP]). Intrasubject analyses were conducted for 48 individuals (4 controls, 11 AR, 8 CRSwNP, and 15 CRSwNP). There was considerable intersubject microbiota variability, but intrasubject profiles were similar (p = 0.001, nonparametric t test). Intrasubject bacterial diversity was significantly reduced in MM of CRSsNP subjects compared to IM samples (p = 0.022, nonparametric t test). CRSsNP MM samples were enriched in Streptococcus, Haemophilus, and Fusobacterium spp. but exhibited loss of diversity compared to healthy, CRSwNP, and AR subject-samples (p < 0.05; nonparametric t test). CRSwNP patients were enriched in Staphylococcus, Alloiococcus, and Corynebacterium spp. CONCLUSION This study presents the sinonasal microbiome profile in one of the larger populations of non-CRS and CRS subjects, and is the first office-based cohort in the literature. In contrast to healthy, AR, and CRSwNP subjects, CRSsNP MM samples exhibited decreased microbiome diversity and anaerobic enrichment. CRSsNP MM samples had reduced diversity compared to same-subject IM samples, a novel finding.
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Affiliation(s)
- Devyani Lal
- Department of Otolaryngology-Head and Neck Surgery, Mayo Clinic in Arizona, Phoenix, AZ
| | - Paul Keim
- Translational Genomics Research Institute, Flagstaff, AZ.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Josie Delisle
- Translational Genomics Research Institute, Flagstaff, AZ
| | - Bridget Barker
- Translational Genomics Research Institute, Flagstaff, AZ.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ
| | - Matthew A Rank
- Division of Allergy, Asthma, and Clinical Immunology, Mayo Clinic in Arizona, Scottsdale, AZ
| | - Nicholas Chia
- Center for Individualized Medicine, Microbiome Program, Mayo Clinic, Rochester, MN
| | - James M Schupp
- Translational Genomics Research Institute, Flagstaff, AZ
| | - John D Gillece
- Translational Genomics Research Institute, Flagstaff, AZ
| | - Emily K Cope
- Translational Genomics Research Institute, Flagstaff, AZ.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
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Rodrigues Hoffmann A. The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals. Vet Dermatol 2017; 28:60-e15. [DOI: 10.1111/vde.12408] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Aline Rodrigues Hoffmann
- Dermatopathology Specialty Service; Department of Veterinary Pathobiology; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; 4467 TAMU College Station TX 77843 USA
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Rotenberg BW. Inverted papilloma: The stubbornly persistent tumor of the sinonasal cavity. Am J Rhinol Allergy 2016; 30:77-8. [PMID: 26980387 DOI: 10.2500/ajra.2016.30.4309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Jervis Bardy J, Psaltis AJ. Next Generation Sequencing and the Microbiome of Chronic Rhinosinusitis: A Primer for Clinicians and Review of Current Research, Its Limitations, and Future Directions. Ann Otol Rhinol Laryngol 2016; 125:613-21. [PMID: 27056556 DOI: 10.1177/0003489416641429] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Microbiomics in chronic diseases, including chronic rhinosinusitis (CRS), have undergone rapid advances in recent times. The introduction of Next Generation Sequencing (NGS) technology has produced significant clinical insights regarding the bacteriology of these conditions. We review studies that have used 16S rRNA sequencing to specifically investigate the microbiota profiles of patients with CRS in a variety of contexts. METHODS Literature review using the CINAHL, MEDLINE, PUBMED, and the Cochrane databases. Papers utilizing 16S-sequencing technology on CRS specimens published between January 1, 1995, and October 31, 2015, were included. Studies limited to only healthy controls were excluded. RESULTS Consistent with published studies using non-NGS techniques, the main genera commonly identified from the sinuses of CRS patients included Staphylococcus, Propionibacterium, and Corynebacterium. The microbiome of CRS patients had lower bacterial diversity compared to controls in a number of studies. Also consistent with non-NGS-based studies, Staphylococcus was implicated as an important genus, with highly colonized patients having worse surgical outcomes. Conflicting reports of antibiotic effects on the CRS microbiome were observed. Sampling methods were well investigated, many of the studies reviewed failed to include important methodological detail. CONCLUSION While 16S sequencing is a novel microbiological laboratory method, current studies have confirmed our existing understanding of bacteriology of CRS without providing significant additional clinical insight. Complementing 16S studies with more complex NGS methods while developing robust clinical studies aimed at shifting the disrupted CRS microbiome will provide researches with the opportunity to derive further clinical insight and develop new therapeutic targets.
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Affiliation(s)
- Jake Jervis Bardy
- Department of Otolaryngology-Head & Neck Surgery, The Queen Elizabeth Hospital and The University of Adelaide, Adelaide, South Australia
| | - Alkis J Psaltis
- Department of Otolaryngology-Head & Neck Surgery, The Queen Elizabeth Hospital and The University of Adelaide, Adelaide, South Australia
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