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Rubio-Portillo E, Orts D, Llorca E, Fernández C, Antón J, Ferrer C, Gálvez B, Esteban V, Revelles E, Pérez-Martín C, Gómez-Imbernón E, Adsuar J, Piqueras P, Amat B, Franco J, Colom MF. The Domestic Environment and the Lung Mycobiome. Microorganisms 2020; 8:E1717. [PMID: 33147738 DOI: 10.3390/microorganisms8111717] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/16/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022] Open
Abstract
This study analyzes the relationship between the mycobiome of the Lower Respiratory Tract (LRT) and the fungi in the domestic environment. Samples studied consisted of Broncho-Alveolar Lavage (BAL) from 45 patients who underwent bronchoscopy for different diagnostic purposes, and dust and air from the houses (ENV) of 20 of them (44.4%). Additionally, five bronchoscopes (BS) were also analyzed and negative controls were included for every procedure. All samples were processed for DNA extraction and cultures, which were performed in Sabouraud Dextrose and Potato Dextrose Agar. The fungal Internal Transcribed Spacer (ITS2) was sequenced by the Solexa/Illumina system and sequences were analyzed by QIIME 1.8.0 and compared with the UNITE Database for identification. The similarity between the two fungal communities (BAL and ENV) for a specific patient was assessed via the percentage of coincidence in the detection of specific operational taxonomic units (OTUs), and about 75% of co-occurrence was detected between the mycobiome of the LRT and the houses. Cultures confirmed the presence of the core mycobiome species. However, the low rate of isolation from BAL suggests that most of its mycobiome corresponds to non-culturable cells. This likely depends on the patient’s immune system activity and inflammatory status.
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Simon-Soro A, Sohn MB, McGinniss JE, Imai I, Brown MC, Knecht VR, Bailey A, Clarke EL, Cantu E, Li H, Bittinger K, Diamond JM, Christie JD, Bushman FD, Collman RG. Upper Respiratory Dysbiosis with a Facultative-dominated Ecotype in Advanced Lung Disease and Dynamic Change after Lung Transplant. Ann Am Thorac Soc 2019; 16:1383-91. [PMID: 31415219 DOI: 10.1513/AnnalsATS.201904-299OC] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Rationale: The oropharyngeal microbiome is a primary source of lung microbiota, contributes to lower respiratory infection, and is also a driver of oral health.Objectives: We sought to understand oropharyngeal microbial communities in advanced lung disease, community dynamics after lung transplantation, and ecological features of dysbiosis.Methods: Oropharyngeal wash samples were obtained from individuals with end-stage disease awaiting transplantation (n = 22) and longitudinally from individuals at 6 weeks, 3 months, and 6 months after transplantation (n = 33), along with healthy control subjects (n = 14). Bacterial 16S and fungal internal transcribed spacer rRNA regions were deep-sequenced, and bacterial community respiratory patterns were imputed from taxonomic composition.Results: Healthy subjects' oropharyngeal microbiomes showed a gradient of community types reflecting relative enrichment of strictly anaerobic, aerobic, or facultative anaerobic bacteria. Patients with end-stage lung disease showed severe dysbiosis by both taxonomic composition and respiration phenotypes, with reduced richness and diversity, increased facultative and decreased aerobic bacteria, and absence of communities characterized by obligate aerobes. In patients at 6 weeks and 3 months post-transplant, richness and diversity were intermediate between healthy and pretransplant subjects, with near-normal distribution of community types. However, by 6 months post-transplant, oropharyngeal wash resembled the low-diversity facultative-dominated profile of pretransplant subjects. Community ecotype correlated with Candida abundance.Conclusions: End-stage lung disease is associated with marked upper respiratory tract dysbiosis involving both community structure and respiratory metabolism profiles of constituent bacteria. Dynamic changes occur after lung transplantation, with partial normalization early but later appearance of severe dysbiosis similar to pretransplant patients. Aberrant oropharyngeal communities may predispose to abnormal lung microbiota and infection risk both in advanced lung disease and after transplantation.
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53
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Zinter MS, Dvorak CC, Mayday MY, Iwanaga K, Ly NP, McGarry ME, Church GD, Faricy LE, Rowan CM, Hume JR, Steiner ME, Crawford ED, Langelier C, Kalantar K, Chow ED, Miller S, Shimano K, Melton A, Yanik GA, Sapru A, DeRisi JL. Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children. Clin Infect Dis 2020; 68:1847-1855. [PMID: 30239621 PMCID: PMC6784263 DOI: 10.1093/cid/ciy802] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children. METHODS We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort. RESULTS We identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001). CONCLUSIONS An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.
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Affiliation(s)
- Matt S Zinter
- Division of Critical Care, University of California, San Francisco School of Medicine
| | - Christopher C Dvorak
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Madeline Y Mayday
- Division of Critical Care, University of California, San Francisco School of Medicine
| | - Kensho Iwanaga
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Ngoc P Ly
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Meghan E McGarry
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Gwynne D Church
- Division of Pulmonology, Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco School of Medicine
| | - Lauren E Faricy
- Division of Pulmonology, Department of Pediatrics, University of Vermont School of Medicine, Burlington
| | - Courtney M Rowan
- Division of Critical Care, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis
| | - Janet R Hume
- Division of Critical Care, University of Minnesota School of Medicine, Minneapolis
| | - Marie E Steiner
- Division of Critical Care, University of Minnesota School of Medicine, Minneapolis.,Hematology/Oncology, Department of Pediatrics, Masonic Children's Hospital, University of Minnesota School of Medicine, Minneapolis
| | - Emily D Crawford
- Chan Zuckerberg Biohub, University of California-San Francisco School of Medicine.,Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Charles Langelier
- Division of Infectious Diseases, Department of Internal Medicine, University of California-San Francisco School of Medicine
| | - Katrina Kalantar
- Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Eric D Chow
- Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
| | - Steve Miller
- Department of Laboratory Medicine, University of California-San Francisco School of Medicine
| | - Kristen Shimano
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Alexis Melton
- Division of Allergy, Immunology, and Blood & Marrow Transplantation, University of California, San Francisco School of Medicine
| | - Gregory A Yanik
- Division of Oncology, Department of Pediatrics, Motts Children's Hospital, University of Michigan School of Medicine, Ann Arbor
| | - Anil Sapru
- Division of Critical Care, University of California, San Francisco School of Medicine.,Division of Critical Care, Department of Pediatrics, Mattel Children's Hospital, University of California-Los Angeles, Geffen School of Medicine
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, University of California-San Francisco School of Medicine.,Department of Biochemistry & Biophysics, University of California-San Francisco School of Medicine
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54
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Martinu T, Koutsokera A, Benden C, Cantu E, Chambers D, Cypel M, Edelman J, Emtiazjoo A, Fisher AJ, Greenland JR, Hayes D, Hwang D, Keller BC, Lease ED, Perch M, Sato M, Todd JL, Verleden S, von der Thüsen J, Weigt SS, Keshavjee S. International Society for Heart and Lung Transplantation consensus statement for the standardization of bronchoalveolar lavage in lung transplantation. J Heart Lung Transplant 2020; 39:1171-1190. [PMID: 32773322 PMCID: PMC7361106 DOI: 10.1016/j.healun.2020.07.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 01/09/2023] Open
Abstract
Bronchoalveolar lavage (BAL) is a key clinical and research tool in lung transplantation (LTx). However, BAL collection and processing are not standardized across LTx centers. This International Society for Heart and Lung Transplantation-supported consensus document on BAL standardization aims to clarify definitions and propose common approaches to improve clinical and research practice standards. The following 9 areas are covered: (1) bronchoscopy procedure and BAL collection, (2) sample handling, (3) sample processing for microbiology, (4) cytology, (5) research, (6) microbiome, (7) sample inventory/tracking, (8) donor bronchoscopy, and (9) pediatric considerations. This consensus document aims to harmonize clinical and research practices for BAL collection and processing in LTx. The overarching goal is to enhance standardization and multicenter collaboration within the international LTx community and enable improvement and development of new BAL-based diagnostics.
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Affiliation(s)
- Tereza Martinu
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, Ontario, Canada.
| | - Angela Koutsokera
- Lung Transplant Program, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada; Lung Transplant Program, Division of Pulmonology, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Edward Cantu
- Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel Chambers
- Lung Transplant Program, The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Marcelo Cypel
- Lung Transplant Program, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Jeffrey Edelman
- Lung Transplant Program, Puget Sound VA Medical Center, Seattle, Washington
| | - Amir Emtiazjoo
- Lung Transplant Program, University of Florida, Gainesville, Florida
| | - Andrew J Fisher
- Institute of Transplantation, Newcastle Upon Tyne Hospitals and Newcastle University, United Kingdom
| | - John R Greenland
- Department of Medicine, VA Health Care System, San Francisco, California
| | - Don Hayes
- Lung Transplant Program, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - David Hwang
- Department of Pathology, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Brian C Keller
- Lung Transplant Program, Wexner Medical Center, The Ohio State University, Columbus, Ohio
| | - Erika D Lease
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, Washington
| | - Michael Perch
- Lung Transplant Program, Rigshospitalet, Copenhagen, Denmark
| | - Masaaki Sato
- Department of Surgery, University of Tokyo, Tokyo, Japan
| | - Jamie L Todd
- Lung Transplant Program, Duke University Medical Center, Durham, North Carolina
| | - Stijn Verleden
- Laboratory of Pneumology, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - S Samuel Weigt
- Lung Transplant Program, University of California Los Angeles, Los Angeles, California
| | - Shaf Keshavjee
- Lung Transplant Program, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
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Abstract
Mycobiota are inseparable from human health, shaking up the unique position held by bacteria among microorganisms. What is surprising is that this seemingly small species can trigger huge changes in the human body. Dysbiosis and invasion of mycobiota are confirmed to cause disease in different parts of the body. Meanwhile, our body also produces corresponding immune changes upon mycobiota infection. Several recent studies have made a connection between intestinal mycobiota and the human immune system. In this review, we focus on questions related to mycobiota, starting with an introduction of select species, then we summarize the typical diseases caused by mycobiota in different parts of the human body. Moreover, we constructed a framework for the human anti-fungal immune system based on genetics and immunology. Finally, the progression of fungal detection methods is also reviewed.
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Affiliation(s)
- Di Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China
| | - Ying Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China
| | - Sunan Shen
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yayi Hou
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Yugen Chen
- Department of Colorectal Surgery, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Tingting Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing, China,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China,CONTACT Tingting Wang The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School of Nanjing University, Nanjing210093, China
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Garcia-Nuñez M, Garcia-Gonzalez M, Pomares X, Montón C, Millares L, Quero S, Prina E, Asensio O, Bosque M, Capilla S, Cuevas O, Monsó E. The Respiratory Microbiome in Cystic Fibrosis: Compartment Patterns and Clinical Relationships in Early Stage Disease. Front Microbiol 2020; 11:1463. [PMID: 32695090 PMCID: PMC7339930 DOI: 10.3389/fmicb.2020.01463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/04/2020] [Indexed: 11/28/2022] Open
Abstract
We compared the bacterial microbiomes lodged in the bronchial tree, oropharynx and nose of patients with early stage cystic fibrosis (CF) not using chronic antibiotics, determining their relationships with lung function and exacerbation frequency. CF patients were enrolled in a cohort study during stability and were checked regularly over the following 9 months. Upper respiratory samples (sputum [S], oropharyngeal swab [OP] and nasal washing [N]) were collected at the first visit and every 3 months. 16S rRNA gene amplification and sequencing was performed and analyzed with QIIME. Seventeen CF patients were enrolled (16.6 SD 9.6 years). Alpha-diversity of bacterial communities between samples was significantly higher in S than in OP (Shannon index median 4.6 [IQR: 4.1–4.9] vs. 3.7 [IQR: 3-1-4.1], p = 0.003/Chao 1 richness estimator median 97.75 [IQR: 85.1–110.9] vs. 43.9 [IQR: 31.7–59.9], p = 0.003) and beta-diversity analysis also showed significant differences in the microbial composition of both respiratory compartments (Adonis test of Bray Curtis dissimilarity matrix, p = 0.001). Dominant taxa were found at baseline in five patients (29.4%), who showed lower forced expiratory volume in the first second (FEV1%, mean 74.8 [SD 19] vs. 97.2 [SD 17.8], p = 0.035, Student t test). The Staphylococcus genus had low RAs in most samples (median 0.26% [IQR 0.01–0.69%]), but patients with RA > 0.26% of Staphylococcus in bronchial secretions suffered more exacerbations during follow-up (median 2 [IQR 1–2.25] vs. 0 [0–1], p = 0.026. Mann–Whitney U test), due to S. aureus in more than a half of the cases, microorganism that often persists as bronchial colonized in these patients (9/10 [90%] vs. 2/7 [28.6%], p = 0.034, Fisher’s exact test). In conclusion, the bronchial microbiome had significantly higher diversity than the microbial flora lodged in the oropharynx in early stage CF. Although the RA of the Staphylococcus genus was low in bronchial secretions and did not reach a dominance pattern, slight overrepresentations of this genus was associated with higher exacerbation frequencies in these patients.
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Affiliation(s)
- Marian Garcia-Nuñez
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Miguel Garcia-Gonzalez
- Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain.,Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Xavier Pomares
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Concepción Montón
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Laura Millares
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Infectious and Respiratory Disease Research Group, Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Sara Quero
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Infectious and Respiratory Disease Research Group, Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Elena Prina
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Oscar Asensio
- Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain.,Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Montserrat Bosque
- Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain.,Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Silvia Capilla
- Department of Microbiology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Oscar Cuevas
- Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Eduard Monsó
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Universitat Autonoma de Barcelona, Barcelona, Spain
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Miao Q, Ma Y, Wang Q, Pan J, Zhang Y, Jin W, Yao Y, Su Y, Huang Y, Wang M, Li B, Li H, Zhou C, Li C, Ye M, Xu X, Li Y, Hu B. Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice. Clin Infect Dis 2019; 67:S231-S240. [PMID: 30423048 DOI: 10.1093/cid/ciy693] [Citation(s) in RCA: 427] [Impact Index Per Article: 85.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) was suggested to potentially replace traditional microbiological methodology because of its comprehensiveness. However, clinical experience with application of the test is relatively limited. Methods From April 2017 to December 2017, 511 specimens were collected, and their retrospective diagnoses were classified into infectious disease (347 [67.9%]), noninfectious disease (119 [23.3%]), and unknown cases (45 [8.8%]). The diagnostic performance of pathogens was compared between mNGS and culture. The effect of antibiotic exposure on detection rate was also assessed. Results The sensitivity and specificity of mNGS for diagnosing infectious disease were 50.7% and 85.7%, respectively, and these values outperformed those of culture, especially for Mycobacterium tuberculosis (odds ratio [OR], 4 [95% confidence interval {CI}, 1.7-10.8]; P < .01), viruses (mNGS only; P < .01), anaerobes (OR, ∞ [95% CI, 1.71-∞]; P < .01) and fungi (OR, 4.0 [95% CI, 1.6-10.3]; P < .01). Importantly, for mNGS-positive cases where the conventional method was inconclusive, 43 (61%) cases led to diagnosis modification, and 41 (58%) cases were not covered by empirical antibiotics. For cases where viruses were identified, broad-spectrum antibiotics were commonly administered (14/27), and 10 of 27 of these cases were suspected to be inappropriate. Interestingly, the sensitivity of mNGS was superior to that of culture (52.5% vs 34.2%; P < .01) in cases with, but not without, antibiotic exposure. Conclusions mNGS could yield a higher sensitivity for pathogen identification and is less affected by prior antibiotic exposure, thereby emerging as a promising technology for detecting infectious diseases.
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Affiliation(s)
- Qing Miao
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Yuyan Ma
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Qingqing Wang
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Yao Zhang
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Wenting Jin
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Yumeng Yao
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Yi Su
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Yingnan Huang
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Mengran Wang
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Bing Li
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Huaying Li
- Department of Microbiology, Zhongshan Hospital of Fudan University
| | - Chunmei Zhou
- Department of Microbiology, Zhongshan Hospital of Fudan University
| | - Chun Li
- Department of Respiratory, Zhongshan Hospital of Fudan University
| | - Maosong Ye
- Department of Respiratory, Zhongshan Hospital of Fudan University
| | - Xiaoling Xu
- BGI China, Shanghai, People's Republic of China
| | - Yongjun Li
- BGI China, Shanghai, People's Republic of China
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
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58
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Li XV, Leonardi I, Iliev ID. Gut Mycobiota in Immunity and Inflammatory Disease. Immunity 2019; 50:1365-1379. [PMID: 31216461 DOI: 10.1016/j.immuni.2019.05.023] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/01/2019] [Accepted: 05/29/2019] [Indexed: 02/08/2023]
Abstract
The mammalian intestine is colonized by a wealth of microorganisms-including bacteria, viruses, protozoa, and fungi-that are all integrated into a functional trans-kingdom community. Characterization of the composition of the fungal community-the mycobiota-has advanced further than the much-needed mechanistic studies. Recent findings have revealed roles for the gut mycobiota in the regulation of host immunity and in the development and progression of human diseases of inflammatory origin. We review these findings here while placing them in the context of the current understanding of the pathways and cellular networks that induce local and systemic immune responses to fungi in the gastrointestinal tract. We discuss gaps in knowledge and argue for the importance of considering bacteria-fungal interactions as we aim to define the roles of mycobiota in immune homeostasis and immune-associated pathologies.
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Affiliation(s)
- Xin V Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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59
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White PL. Recent advances and novel approaches in laboratory-based diagnostic mycology. Med Mycol 2019; 57:S259-S266. [PMID: 31292661 DOI: 10.1093/mmy/myy159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/29/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022] Open
Abstract
The field of diagnostic mycology represents much more than culture and microscopy and is rapidly embracing novel techniques and strategies to help overcome the limitations of conventional approaches. Commercial molecular assays increase the applicability of PCR testing and may identify markers of antifungal resistance, which are of great clinical concern. Lateral flow assays simplify testing and turn-around time, with potential for point of care testing, while proximity ligation assays embrace the sensitivity of molecular testing with the specificity of antibody detection. The first evidence of patient risk stratification is being described and together with the era of next generation sequencing represents an exciting time in mycology.
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Affiliation(s)
- P Lewis White
- Mycology Reference Laboratory, Public Health Wales, Microbiology Cardiff, Cardiff, United Kingdom
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Gangneux JP, Guegan H, Vandenborght LE, Buffet-Bataillon S, Enaud R, Delhaes L. A European ECMM-ESCMID survey on goals and practices for mycobiota characterisation using next-generation sequencing. Mycoses 2019; 62:1096-1099. [PMID: 31498487 DOI: 10.1111/myc.12999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022]
Abstract
Although substantial efforts have been made to investigate about the composition of the microbiota, fungi that constitute the mycobiota play a pivotal role in maintaining microbial communities and physiological processes in the body. Here, we conducted an international survey focusing on laboratory's current procedures regarding their goals and practices of mycobiota characterisation using NGS. A questionnaire was proposed to laboratories affiliated to working groups from ECMM (NGS study group) and ESCMID (ESGHAMI and EFISG study groups). Twenty-six questionnaires from 18 countries were received. The use of NGS to characterise the mycobiota was not in routine for most of the laboratories (N = 23, 82%), and the main reason of using NGS was primary to understand the pathophysiology of a dysbiosis (N = 20), to contribute to a diagnosis (N = 16) or to implement a therapeutic strategy (N = 12). Other reported reasons were to evaluate the exposome (environmental studies) (N = 10) or to investigate epidemics (N = 8). Sputum is the main sample studied, and cystic fibrosis represents a major disease studied via the analysis of pulmonary microbiota. No consensus has emerged for the choice of the targets with 18S, ITS1 and ITS2 used alternatively among the laboratories. Other answers are detailed in the manuscript. We report a photography of mycobiota analysis that may become a major tool in the near future. We can draw some conclusions on the diversity of approaches within the answers of the 27 laboratories and underline the need for standardisation.
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Affiliation(s)
- Jean-Pierre Gangneux
- CHU Rennes, Univ Rennes, Inserm, Irset (Institut de Recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Hélène Guegan
- CHU Rennes, Univ Rennes, Inserm, Irset (Institut de Recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Louise-Eva Vandenborght
- CHU de Bordeaux, Université de Bordeaux, Inserm, Center for Cardiothoracic Research of Bordeaux, U1045, CIC 1401, Bordeaux, France
| | - Sylvie Buffet-Bataillon
- CHU Rennes, Univ Rennes, Inserm, Irset (Institut de Recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Raphael Enaud
- CHU de Bordeaux, Université de Bordeaux, Inserm, Center for Cardiothoracic Research of Bordeaux, U1045, CIC 1401, Bordeaux, France
| | - Laurence Delhaes
- CHU de Bordeaux, Université de Bordeaux, Inserm, Center for Cardiothoracic Research of Bordeaux, U1045, CIC 1401, Bordeaux, France
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Abstract
The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg Lluís Companys 23, 08010 Barcelona, Spain
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Weaver D, Gago S, Bromley M, Bowyer P. The Human Lung Mycobiome in Chronic Respiratory Disease: Limitations of Methods and Our Current Understanding. Curr Fungal Infect Rep 2019; 13:109-19. [DOI: 10.1007/s12281-019-00347-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Karstens L, Asquith M, Davin S, Fair D, Gregory WT, Wolfe AJ, Braun J, McWeeney S. Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments. mSystems 2019; 4:e00290-19. [PMID: 31164452 DOI: 10.1128/mSystems.00290-19] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The relative scarcity of microbes in low-microbial-biomass environments makes accurate determination of community composition challenging. Identifying and controlling for contaminant bacterial DNA are critical steps in understanding microbial communities from these low-biomass environments. Our study introduces the use of a mock community dilution series as a positive control and evaluates four computational strategies that can identify contaminants in 16S rRNA gene sequencing experiments in order to remove them from downstream analyses. The appropriate computational approach for removing contaminant sequences from an experiment depends on prior knowledge about the microbial environment under investigation and can be evaluated with a dilution series of a mock microbial community. Microbial communities are commonly studied using culture-independent methods, such as 16S rRNA gene sequencing. However, one challenge in accurately characterizing microbial communities is exogenous bacterial DNA contamination, particularly in low-microbial-biomass niches. Computational approaches to identify contaminant sequences have been proposed, but their performance has not been independently evaluated. To identify the impact of decreasing microbial biomass on polymicrobial 16S rRNA gene sequencing experiments, we created a mock microbial community dilution series. We evaluated four computational approaches to identify and remove contaminants, as follows: (i) filtering sequences present in a negative control, (ii) filtering sequences based on relative abundance, (iii) identifying sequences that have an inverse correlation with DNA concentration implemented in Decontam, and (iv) predicting the sequence proportion arising from defined contaminant sources implemented in SourceTracker. As expected, the proportion of contaminant bacterial DNA increased with decreasing starting microbial biomass, with 80.1% of the most diluted sample arising from contaminant sequences. Inclusion of contaminant sequences led to overinflated diversity estimates and distorted microbiome composition. All methods for contaminant identification successfully identified some contaminant sequences, which varied depending on the method parameters used and contaminant prevalence. Notably, removing sequences present in a negative control erroneously removed >20% of expected sequences. SourceTracker successfully removed over 98% of contaminants when the experimental environments were well defined. However, SourceTracker misclassified expected sequences and performed poorly when the experimental environment was unknown, failing to remove >97% of contaminants. In contrast, the Decontam frequency method did not remove expected sequences and successfully removed 70 to 90% of the contaminants. IMPORTANCE The relative scarcity of microbes in low-microbial-biomass environments makes accurate determination of community composition challenging. Identifying and controlling for contaminant bacterial DNA are critical steps in understanding microbial communities from these low-biomass environments. Our study introduces the use of a mock community dilution series as a positive control and evaluates four computational strategies that can identify contaminants in 16S rRNA gene sequencing experiments in order to remove them from downstream analyses. The appropriate computational approach for removing contaminant sequences from an experiment depends on prior knowledge about the microbial environment under investigation and can be evaluated with a dilution series of a mock microbial community.
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McGinniss JE, Imai I, Simon-Soro A, Brown MC, Knecht VR, Frye L, Ravindran PM, Dothard MI, Wadell DA, Sohn MB, Li H, Christie JD, Diamond JM, Haas AR, Lanfranco AR, DiBardino DM, Bushman FD, Collman RG. Molecular analysis of the endobronchial stent microbial biofilm reveals bacterial communities that associate with stent material and frequent fungal constituents. PLoS One 2019; 14:e0217306. [PMID: 31141557 PMCID: PMC6541290 DOI: 10.1371/journal.pone.0217306] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/08/2019] [Indexed: 12/19/2022] Open
Abstract
Endobronchial stents are increasingly used to treat airway complications in multiple conditions including lung transplantation but little is known about the biofilms that form on these devices. We applied deep sequencing to profile luminal biofilms of 46 endobronchial stents removed from 20 subjects primarily with lung transplantation-associated airway compromise. Microbial communities were analyzed by bacterial 16S rRNA and fungal ITS marker gene sequencing. Corynebacterium was the most common bacterial taxa across biofilm communities. Clustering analysis revealed three bacterial biofilm types: one low diversity and dominated by Corynebacterium; another was polymicrobial and characterized by Staphylococcus; and the third was polymicrobial and associated with Pseudomonas, Streptococcus, and Prevotella. Biofilm type was significantly correlated with stent material: covered metal with the Staphylococcus-type biofilm, silicone with the Corynebacterium-dominated biofilm, and uncovered metal with the polymicrobial biofilm. Subjects with sequential stents had frequent transitions between community types. Fungal analysis found Candida was most prevalent, Aspergillus was common and highly enriched in two of three stents associated with airway anastomotic dehiscence, and fungal taxa not typically considered pathogens were highly enriched in some stents. Thus, molecular analysis revealed a complex and dynamic endobronchial stent biofilm with three bacterial types that associate with stent material, a central role for Corynebacterium, and that both expected and unexpected fungi inhabit this unique niche. The current work provides a foundation for studies to investigate the relationship between stent biofilm composition and clinical outcomes, mechanisms of biofilm establishment, and strategies for improved stent technology and use in airway compromise.
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Affiliation(s)
- John E. McGinniss
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ize Imai
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Aurea Simon-Soro
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Melanie C. Brown
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Vincent R. Knecht
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Laura Frye
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Priyanka M. Ravindran
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marisol I. Dothard
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dylan A. Wadell
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael B. Sohn
- Department of Epidemiology, Biostatistics and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hongzhe Li
- Department of Epidemiology, Biostatistics and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jason D. Christie
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Epidemiology, Biostatistics and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joshua M. Diamond
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrew R. Haas
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anthony R. Lanfranco
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - David M. DiBardino
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RGC); (FDB)
| | - Ronald G. Collman
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RGC); (FDB)
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Zinter MS, Mayday MY, Ryckman KK, Jelliffe-Pawlowski LL, DeRisi JL. Towards precision quantification of contamination in metagenomic sequencing experiments. Microbiome 2019; 7:62. [PMID: 30992055 PMCID: PMC6469116 DOI: 10.1186/s40168-019-0678-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) experiments involving small amounts of nucleic acid input are highly susceptible to erroneous conclusions resulting from unintentional sequencing of occult contaminants, especially those derived from molecular biology reagents. Recent work suggests that, for any given microbe detected by mNGS, an inverse linear relationship between microbial sequencing reads and sample mass implicates that microbe as a contaminant. By associating sequencing read output with the mass of a spike-in control, we demonstrate that contaminant nucleic acid can be quantified in order to identify the mass contributions of each constituent. In an experiment using a high-resolution (n = 96) dilution series of HeLa RNA spanning 3-logs of RNA mass input, we identified a complex set of contaminants totaling 9.1 ± 2.0 attograms. Given the competition between contamination and the true microbiome in ultra-low biomass samples such as respiratory fluid, quantification of the contamination within a given batch of biological samples can be used to determine a minimum mass input below which sequencing results may be distorted. Rather than completely censoring contaminant taxa from downstream analyses, we propose here a statistical approach that allows separation of the true microbial components from the actual contribution due to contamination. We demonstrate this approach using a batch of n = 97 human serum samples and note that despite E. coli contamination throughout the dataset, we are able to identify a patient sample with significantly more E. coli than expected from contamination alone. Importantly, our method assumes no prior understanding of possible contaminants, does not rely on any prior collection of environmental or reagent-only sequencing samples, and does not censor potentially clinically relevant taxa, thus making it a generalized approach to any kind of metagenomic sequencing, for any purpose, clinical or otherwise.
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Affiliation(s)
- M. S. Zinter
- Department of Pediatrics, Division of Critical Care, University of California, San Francisco School of Medicine, Benioff Children’s Hospital, San Francisco, CA USA
| | - M. Y. Mayday
- Department of Pediatrics, Division of Critical Care, University of California, San Francisco School of Medicine, Benioff Children’s Hospital, San Francisco, CA USA
| | - K. K. Ryckman
- Department of Epidemiology, University of Iowa, College of Public Health, Iowa City, IA USA
| | - L. L. Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California, San Francisco School of Medicine, San Francisco, CA USA
- California Preterm Birth Initiative, University of California San Francisco School of Medicine, San Francisco, CA USA
| | - J. L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco School of Medicine, San Francisco, CA USA
- Chan Zuckerberg Biohub, San Francisco, CA USA
- 1700 4th St, 403C, Campus Box 2542, San Francisco, CA 94158-2330 USA
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66
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Clarke EL, Lauder AP, Hofstaedter CE, Hwang Y, Fitzgerald AS, Imai I, Biernat W, Rękawiecki B, Majewska H, Dubaniewicz A, Litzky LA, Feldman MD, Bittinger K, Rossman MD, Patterson KC, Bushman FD, Collman RG. Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low-Microbial Content Samples. Am J Respir Crit Care Med 2019; 197:225-234. [PMID: 28846439 DOI: 10.1164/rccm.201705-0891oc] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
RATIONALE The etiology of sarcoidosis is unknown, but microbial agents are suspected as triggers. OBJECTIVES We sought to identify bacterial, fungal, or viral lineages in specimens from patients with sarcoidosis enriched relative to control subjects using metagenomic DNA sequencing. Because DNA from environmental contamination contributes disproportionately to samples with low authentic microbial content, we developed improved methods for filtering environmental contamination. METHODS We analyzed specimens from subjects with sarcoidosis (n = 93), control subjects without sarcoidosis (n = 72), and various environmental controls (n = 150). Sarcoidosis specimens consisted of two independent sets of formalin-fixed, paraffin-embedded lymph node biopsies, BAL, Kveim reagent, and fresh granulomatous spleen from a patient with sarcoidosis. All specimens were analyzed by bacterial 16S and fungal internal transcribed spacer ribosomal RNA gene sequencing. In addition, BAL was analyzed by shotgun sequencing of fractions enriched for viral particles, and Kveim and spleen were subjected to whole-genome shotgun sequencing. MEASUREMENTS AND MAIN RESULTS In one tissue set, fungi in the Cladosporiaceae family were enriched in sarcoidosis compared with nonsarcoidosis tissues; in the other tissue set, we detected enrichment of several bacterial lineages in sarcoidosis but not Cladosporiaceae. BAL showed limited enrichment of Aspergillus fungi. Several microbial lineages were detected in Kveim and spleen, including Cladosporium. No microbial lineage was enriched in more than one sample type after correction for multiple comparisons. CONCLUSIONS Metagenomic sequencing revealed enrichment of microbes in single types of sarcoidosis samples but limited concordance across sample types. Statistical analysis accounting for environmental contamination was essential to avoiding false positives.
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Affiliation(s)
| | | | - Casey E Hofstaedter
- 2 Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; and
| | | | | | | | | | | | | | - Anna Dubaniewicz
- 5 Department of Pulmonology, Medical University of Gdansk, Gdansk, Poland
| | - Leslie A Litzky
- 6 Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Michael D Feldman
- 6 Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kyle Bittinger
- 2 Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; and
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McTaggart LR, Copeland JK, Surendra A, Wang PW, Husain S, Coburn B, Guttman DS, Kus JV. Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis. Front Microbiol 2019; 10:512. [PMID: 30930884 PMCID: PMC6428700 DOI: 10.3389/fmicb.2019.00512] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Invasive fungal infections are an increasingly important cause of human morbidity and mortality. We generated a next-generation sequencing (NGS)-based method designed to detect a wide range of fungi and applied it to analysis of the fungal microbiome (mycobiome) of the lung during fungal infection. Internal transcribed spacer 1 (ITS1) amplicon sequencing and a custom analysis pipeline detected 96% of species from three mock communities comprised of potential fungal lung pathogens with good recapitulation of the expected species distributions (Pearson correlation coefficients r = 0.63, p = 0.004; r = 0.71, p < 0.001; r = 0.62, p = 0.002). We used this pipeline to analyze mycobiomes of bronchoalveolar lavage (BAL) specimens classified as culture-negative (n = 50) or culture-positive (n = 39) for Blastomyces dermatitidis/gilchristii, the causative agent of North America blastomycosis. Detected in 91.4% of the culture-positive samples, Blastomyces dominated (>50% relative abundance) the mycobiome in 68.6% of these culture-positive samples but was absent in culture-negative samples. To overcome any bias in relative abundance due to between-sample variation in fungal biomass, an abundance-weighting calculation was used to normalize the data by accounting for sample-specific PCR cycle number and PCR product concentration data utilized during sample preparation. After normalization, there was a statistically significant greater overall abundance of ITS1 amplicon in the Blastomyces-culture-positive samples versus culture-negative samples. Moreover, the normalization revealed a greater biomass of yeast and environmental fungi in several Blastomyces-culture-positive samples than in the culture-negative samples. Successful detection of Coccidioides, Scedosporium, Phaeoacremonium, and Aspergillus in 6 additional culture-positive BALs by ITS1 amplicon sequencing demonstrates the ability of this method to detect a broad range of fungi from clinical specimens, suggesting that it may be a potentially useful adjunct to traditional fungal microbiological testing for the diagnosis of respiratory mycoses.
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Affiliation(s)
| | - Julia K Copeland
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | | | - Pauline W Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Shahid Husain
- Division of Infectious Diseases, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Julianne V Kus
- Public Health Ontario, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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68
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Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 2018; 6:226. [PMID: 30558668 PMCID: PMC6298009 DOI: 10.1186/s40168-018-0605-2] [Citation(s) in RCA: 1203] [Impact Index Per Article: 200.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/25/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants-DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam ( https://github.com/benjjneb/decontam ), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls. RESULTS Decontam classified amplicon sequence variants (ASVs) in a human oral dataset consistently with prior microscopic observations of the microbial taxa inhabiting that environment and previous reports of contaminant taxa. In metagenomics and marker-gene measurements of a dilution series, decontam substantially reduced technical variation arising from different sequencing protocols. The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants. CONCLUSIONS Decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles of microbial communities at little to no additional cost.
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Affiliation(s)
- Nicole M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Diana M Proctor
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Orofacial Sciences, University of California, San Francisco School of Dentistry, San Francisco, CA, 94143, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Benjamin J Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 456 Research Building, 1060 William Moore Drive, Raleigh, NC, 27607, USA.
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA.
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Knecht VR, McGinniss JE, Shankar HM, Clarke EL, Kelly BJ, Imai I, Fitzgerald AS, Bittinger K, Bushman FD, Collman RG. Molecular analysis of bacterial contamination on stethoscopes in an intensive care unit. Infect Control Hosp Epidemiol 2019; 40:171-7. [PMID: 30560753 DOI: 10.1017/ice.2018.319] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Culture-based studies, which focus on individual organisms, have implicated stethoscopes as potential vectors of nosocomial bacterial transmission. However, the full bacterial communities that contaminate in-use stethoscopes have not been investigated. METHODS We used bacterial 16S rRNA gene deep-sequencing, analysis, and quantification to profile entire bacterial populations on stethoscopes in use in an intensive care unit (ICU), including practitioner stethoscopes, individual-use patient-room stethoscopes, and clean unused individual-use stethoscopes. Two additional sets of practitioner stethoscopes were sampled before and after cleaning using standardized or practitioner-preferred methods. RESULTS Bacterial contamination levels were highest on practitioner stethoscopes, followed by patient-room stethoscopes, whereas clean stethoscopes were indistinguishable from background controls. Bacterial communities on stethoscopes were complex, and community analysis by weighted UniFrac showed that physician and patient-room stethoscopes were indistinguishable and significantly different from clean stethoscopes and background controls. Genera relevant to healthcare-associated infections (HAIs) were common on practitioner stethoscopes, among which Staphylococcus was ubiquitous and had the highest relative abundance (6.8%-14% of contaminating bacterial sequences). Other HAI-related genera were also widespread although lower in abundance. Cleaning of practitioner stethoscopes resulted in a significant reduction in bacterial contamination levels, but these levels reached those of clean stethoscopes in only a few cases with either standardized or practitioner-preferred methods, and bacterial community composition did not significantly change. CONCLUSIONS Stethoscopes used in an ICU carry bacterial DNA reflecting complex microbial communities that include nosocomially important taxa. Commonly used cleaning practices reduce contamination but are only partially successful at modifying or eliminating these communities.
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Ricna D, Lengerova M, Bezdicek M, Kocmanova I, Drgona L, Weinbergerova B, Mayer J, Racil Z. Detection and identification of fungi in bronchoalveolar lavage fluid from immunocompromised patients using panfungal PCR. Folia Microbiol (Praha) 2019; 64:421-8. [PMID: 30535753 DOI: 10.1007/s12223-018-00669-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/29/2018] [Indexed: 01/24/2023]
Abstract
Rapid diagnostics of fungal pneumonia and initiation of appropriate therapy are still challenging. In this study, we used two panfungal assays to test bronchoalveolar lavage fluid (BALF) samples to prove their ability to confirm invasive fungal disease diagnosis and identify causative agents. Two methods targeting different fungal rDNA regions were used, and the obtained PCR products were sequenced directly or after cloning. In total, 106 BALF samples from 104 patients were tested. After sequencing, we obtained 578 sequences. Four hundred thirty-seven sequences were excluded from further analysis due to duplication (n = 335) or similarity with sequences detected in the extraction control sample (n = 102); 141 unique sequences were analyzed. Altogether, 23/141 (16%) of the fungi detected belonged to pathogenic species, and 63/141 (45%) were identified as various yeasts; a variety of environmental or very rare fungal human pathogens represented 29/141 (21%) of the total and 26/141 (18%) were described as uncultured fungus. Panfungal PCR detected fungal species that would be missed by specific methods in only one case (probable cryptococcosis). Panfungal PCR followed by sequencing has limited use for testing BALF samples due to frequent commensal or environmental fungal species pickup.
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71
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Guo M, Jiang W, Luo J, Yang M, Pang X. Analysis of the Fungal Community in Ziziphi Spinosae Semen through High-Throughput Sequencing. Toxins (Basel) 2018; 10:E494. [PMID: 30477258 PMCID: PMC6315384 DOI: 10.3390/toxins10120494] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/14/2018] [Accepted: 11/23/2018] [Indexed: 12/31/2022] Open
Abstract
Ziziphi Spinosae Semen (ZSS) has been widely used in traditional Chinese medicine system for decades. Under proper humidity and temperature, ZSS is easily contaminated by fungi and mycotoxins during harvest, storage, and transport, thereby posing a considerable threat to consumer health. In this study, we first used the Illumina MiSeq PE250 platform and targeted the internal transcribed spacer 2 sequences to investigate the presence of fungi in moldy and normal ZSS samples collected from five producing areas in China. Results showed that all 14 samples tested were contaminated by fungi. Ascomycota was the dominant fungus at the phylum level, accounting for 64.36⁻99.74% of the fungal reads. At the genus level, Aspergillus, Candida, and Wallemia were the most predominant genera, with the relative abundances of 13.52⁻87.87%, 0.42⁻64.56%, and 0.06⁻34.31%, respectively. Meanwhile, 70 fungal taxa were identified at the species level. Among these taxa, three potential mycotoxin-producing fungi, namely, Aspergillusflavus, A. fumigatus, and Penicillium citrinum that account for 0.30⁻36.29%, 0.04⁻7.37%, and 0.01⁻0.80% of the fungal reads, respectively, were detected in all ZSS samples. Moreover, significant differences in fungal communities were observed in the moldy and normal ZSS samples. In conclusion, our results indicated that amplicon sequencing is feasible for the detection and analysis of the fungal community in the ZSS samples. This study used a new approach to survey the fungal contamination in herbal materials. This new approach can provide early warning for mycotoxin contamination in herbal materials, thereby ensuring drug efficacy and safety.
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Affiliation(s)
- Mengyue Guo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Wenjun Jiang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Jiaoyang Luo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Meihua Yang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Xiaohui Pang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
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Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG, Blaser MJ. Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population. Front Microbiol 2018; 9:2533. [PMID: 30405584 PMCID: PMC6208322 DOI: 10.3389/fmicb.2018.02533] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/04/2018] [Indexed: 01/28/2023] Open
Abstract
The human cervicovaginal microbiota resides at an interface between the host and the environment and may affect susceptibility to disease. Puerto Rican women have high human papillomavirus (HPV) infection and cervical cancer rates. We hypothesized that the population structure of the cervicovaginal bacterial and fungal biota changed with cervical squamous intraepithelial lesions and HPV infections. DNA was extracted from cervix, introitus, and anal sites of 62 patients attending high-risk San Juan clinics. The 16S rRNA V4 region and ITS-2 fungal regions were amplified and sequenced using Illumina technology. HPV genotyping was determined by reverse hybridization with the HPV SPF10-LiPA25 kit. HPV prevalence was 84% of which ∼44% subjects were infected with high-risk HPV, ∼35% were co-infected with as many as 9 HPV types and ∼5% were infected with exclusively low-risk HPV types. HPV diversity did not change with cervical dysplasia. Cervical bacteria were more diverse in patients with CIN3 pre-cancerous lesions. We found enrichment of Atopobium vaginae and Gardnerella vaginalis in patients with CIN3 lesions. We found no significant bacterial biomarkers associated with HPV infections. Fungal diversity was significantly higher in cervical samples with high-risk HPV and introitus samples of patients with Atypical Squamous Cells of Undetermined Significance (ASCUS). Fungal biomarker signatures for vagina and cervix include Sporidiobolaceae and Sacharomyces for ASCUS, and Malassezia for high-risk HPV infections. Our combined data suggests that specific cervicovaginal bacterial and fungal populations are related to the host epithelial microenvironment, and could play roles in cervical dysplasia.
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Affiliation(s)
- Filipa Godoy-Vitorino
- Microbiome Lab, Department of Microbiology and Medical Zoology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, United States
- Microbial Ecology and Genomics Laboratory, Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, PR, United States
| | - Josefina Romaguera
- Department of Obstetrics and Gynecology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, United States
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Daniela Vargas-Robles
- Department of Biology, University of Puerto Rico, San Juan, PR, Puerto Rico
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, MPPS, Puerto Ayacucho, Venezuela
| | - Gilmary Ortiz-Morales
- Microbial Ecology and Genomics Laboratory, Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, PR, United States
| | - Frances Vázquez-Sánchez
- Microbial Ecology and Genomics Laboratory, Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, PR, United States
| | | | - Manuel de la Garza-Casillas
- Microbial Ecology and Genomics Laboratory, Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, PR, United States
| | - Magaly Martinez-Ferrer
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
- Department of Pharmaceutical Sciences, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, United States
| | | | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology and of Anthropology, Rutgers University, New Brunswick, NJ, United States
| | - Martin J. Blaser
- Department of Medicine and Department of Microbiology, School of Medicine, New York University, New York, NY, United States
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73
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Hoggard M, Vesty A, Wong G, Montgomery JM, Fourie C, Douglas RG, Biswas K, Taylor MW. Characterizing the Human Mycobiota: A Comparison of Small Subunit rRNA, ITS1, ITS2, and Large Subunit rRNA Genomic Targets. Front Microbiol 2018; 9:2208. [PMID: 30283425 PMCID: PMC6157398 DOI: 10.3389/fmicb.2018.02208] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 08/29/2018] [Indexed: 12/28/2022] Open
Abstract
Interest in the human microbiome has increased dramatically in the last decade. However, much of this research has focused on bacteria, while the composition and roles of their fungal counterparts remain less understood. Furthermore, a variety of methodological approaches have been applied, and the comparability between studies is unclear. This study compared four primer pairs targeting the small subunit (SSU) rRNA (18S), ITS1, ITS2, and large subunit (LSU) rRNA (26S) genomic regions for their ability to accurately characterize fungal communities typical of the human mycobiota. All four target regions of 21 individual fungal mock community taxa were capable of being amplified adequately and sequenced. Mixed mock community analyses revealed marked variability in the ability of each primer pair to accurately characterize a complex community. ITS target regions outperformed LSU and SSU. Of the ITS regions, ITS1 failed to generate sequences for Yarrowia lipolytica and all three Malassezia species when in a mixed community. These findings were further supported in studies of human sinonasal and mouse fecal samples. Based on these analyses, previous studies using ITS1, SSU, or LSU markers may omit key taxa that are identified by the ITS2 marker. Of methods commonly used in human mycobiota studies to date, we recommend selection of the ITS2 marker. Further investigation of more recently developed fungal primer options will be essential to ultimately determine the optimal methodological approach by which future human mycobiota studies ought to be standardized.
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Affiliation(s)
- Michael Hoggard
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Anna Vesty
- School of Medicine, The University of Auckland, Auckland, New Zealand.,Microbiology Laboratory, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Giselle Wong
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Johanna M Montgomery
- Department of Physiology, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Chantelle Fourie
- Department of Physiology, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Richard G Douglas
- School of Medicine, The University of Auckland, Auckland, New Zealand
| | - Kristi Biswas
- School of Medicine, 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, The University of Auckland, Auckland, New Zealand
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74
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Abusleme L, Diaz PI, Freeman AF, Greenwell-Wild T, Brenchley L, Desai JV, Ng WI, Holland SM, Lionakis MS, Segre JA, Kong HH, Moutsopoulos NM. Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis. JCI Insight 2018; 3:122061. [PMID: 30185668 DOI: 10.1172/jci.insight.122061] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/10/2018] [Indexed: 12/19/2022] Open
Abstract
Studies in patients with genetic defects can provide unique insights regarding the role of specific genes and pathways in humans. Patients with defects in the Th17/IL-17 axis, such as patients harboring loss-of-function STAT3 mutations (autosomal-dominant hyper IgE syndrome; AD-HIES) present with recurrent oral fungal infections. Our studies aimed to comprehensively evaluate consequences of STAT3 deficiency on the oral commensal microbiome. We characterized fungal and bacterial communities in AD-HIES in the presence and absence of oral fungal infection compared with healthy volunteers. Analyses of oral mucosal fungal communities in AD-HIES revealed severe dysbiosis with dominance of Candida albicans (C. albicans) in actively infected patients and minimal representation of health-associated fungi and/or opportunists. Bacterial communities also displayed dysbiosis in AD-HIES, particularly in the setting of active Candida infection. Active candidiasis was associated with decreased microbial diversity and enrichment of the streptococci Streptococcus oralis (S. oralis) and S. mutans, suggesting an interkingdom interaction of C. albicans with oral streptococci. Increased abundance of S. mutans was consistent with susceptibility to dental caries in AD-HIES. Collectively, our findings illustrate a critical role for STAT3/Th17 in the containment of C. albicans as a commensal organism and an overall contribution in the establishment of fungal and bacterial oral commensal communities.
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Affiliation(s)
- Loreto Abusleme
- Oral Immunity and Inflammation Unit, NIDCR, NIH, Bethesda, Maryland, USA.,Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Patricia I Diaz
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, UConn Health Center, Farmington, Connecticut, USA
| | | | | | - Laurie Brenchley
- Oral Immunity and Inflammation Unit, NIDCR, NIH, Bethesda, Maryland, USA
| | | | | | | | | | | | - Heidi H Kong
- Cutaneous Microbiome and Inflammation Section, NIAMS, NIH, Bethesda, Maryland, USA
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75
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Abusleme L, Diaz PI, Freeman AF, Greenwell-Wild T, Brenchley L, Desai JV, Ng WI, Holland SM, Lionakis MS, Segre JA, Kong HH, Moutsopoulos NM. Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis. JCI Insight 2018. [PMID: 30185668 DOI: 10.1172/jci.insight.1220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Studies in patients with genetic defects can provide unique insights regarding the role of specific genes and pathways in humans. Patients with defects in the Th17/IL-17 axis, such as patients harboring loss-of-function STAT3 mutations (autosomal-dominant hyper IgE syndrome; AD-HIES) present with recurrent oral fungal infections. Our studies aimed to comprehensively evaluate consequences of STAT3 deficiency on the oral commensal microbiome. We characterized fungal and bacterial communities in AD-HIES in the presence and absence of oral fungal infection compared with healthy volunteers. Analyses of oral mucosal fungal communities in AD-HIES revealed severe dysbiosis with dominance of Candida albicans (C. albicans) in actively infected patients and minimal representation of health-associated fungi and/or opportunists. Bacterial communities also displayed dysbiosis in AD-HIES, particularly in the setting of active Candida infection. Active candidiasis was associated with decreased microbial diversity and enrichment of the streptococci Streptococcus oralis (S. oralis) and S. mutans, suggesting an interkingdom interaction of C. albicans with oral streptococci. Increased abundance of S. mutans was consistent with susceptibility to dental caries in AD-HIES. Collectively, our findings illustrate a critical role for STAT3/Th17 in the containment of C. albicans as a commensal organism and an overall contribution in the establishment of fungal and bacterial oral commensal communities.
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Affiliation(s)
- Loreto Abusleme
- Oral Immunity and Inflammation Unit, NIDCR, NIH, Bethesda, Maryland, USA
- Faculty of Dentistry, University of Chile, Santiago, Chile
| | - Patricia I Diaz
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, UConn Health Center, Farmington, Connecticut, USA
| | | | | | - Laurie Brenchley
- Oral Immunity and Inflammation Unit, NIDCR, NIH, Bethesda, Maryland, USA
| | | | | | | | | | | | - Heidi H Kong
- Cutaneous Microbiome and Inflammation Section, NIAMS, NIH, Bethesda, Maryland, USA
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76
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Rhee RL, Sreih AG, Najem CE, Grayson PC, Zhao C, Bittinger K, Collman RG, Merkel PA. Characterisation of the nasal microbiota in granulomatosis with polyangiitis. Ann Rheum Dis 2018; 77:1448-1453. [PMID: 29997110 DOI: 10.1136/annrheumdis-2018-213645] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/18/2018] [Accepted: 06/22/2018] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Prior studies have suggested a potential link between nasal microbes and granulomatosis with polyangiitis (GPA; Wegener's), but these studies relied on culture-dependent methods. This study comprehensively examined the entire community of nasal microbiota (bacteria and fungi) in participants with GPA compared with healthy controls using deep sequencing methods. METHODS 16S rRNA and internal transcribed spacer gene sequencing were performed on nasal microbial DNA isolated from nasal swabs of 60 participants with GPA and 41 healthy controls. Alpha and beta diversity were assessed as well as the relative abundance of the most abundant bacterial and fungal taxa. The effects of covariates including disease activity and immunosuppressive therapies on microbial composition were evaluated. RESULTS Compared with controls, participants with GPA had a significantly different microbial composition (weighted UniFrac p=0.04) and lower relative abundance of Propionibacterium acnes and Staphylococcus epidermidis (for both, false discovery rate-corrected p=0.02). Disease activity in GPA was associated with a lower abundance of fungal order Malasseziales compared with participants with GPA in remission (p=0.04) and controls (p=0.01). Use of non-glucocorticoid immunosuppressive therapy was associated with 'healthy' nasal microbiota while participants with GPA who were off immunosuppressive therapy had more dysbiosis (weighted UniFrac p=0.01). No difference in the relative abundance of Staphylococcus aureus was observed between GPA and controls. CONCLUSIONS GPA is associated with an altered nasal microbial composition, at both the bacterial and fungal levels. Use of immunosuppressive therapies and disease remission are associated with healthy microbial communities.
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Affiliation(s)
- Rennie L Rhee
- Division of Rheumatology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Antoine G Sreih
- Division of Rheumatology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Catherine E Najem
- Division of Rheumatology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Peter C Grayson
- Vasculitis Translational Research Program, National Institutes of of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ronald G Collman
- Division of Pulmonary, Allergy, and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Peter A Merkel
- Division of Rheumatology and the Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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77
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Tipton L, Cuenco KT, Huang L, Greenblatt RM, Kleerup E, Sciurba F, Duncan SR, Donahoe MP, Morris A, Ghedin E. Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model. BioData Min 2018; 11:12. [PMID: 29983746 PMCID: PMC6003033 DOI: 10.1186/s13040-018-0173-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/27/2018] [Indexed: 01/28/2023] Open
Abstract
Background Human microbiome studies in clinical settings generally focus on distinguishing the microbiota in health from that in disease at a specific point in time. However, microbiome samples may be associated with disease severity or continuous clinical health indicators that are often assessed at multiple time points. While the temporal data from clinical and microbiome samples may be informative, analysis of this type of data can be problematic for standard statistical methods. Results To identify associations between microbiota and continuous clinical variables measured repeatedly in two studies of the respiratory tract, we adapted a statistical method, the lasso-penalized generalized linear mixed model (LassoGLMM). LassoGLMM can screen for associated clinical variables, incorporate repeated measures of individuals, and address the large number of species found in the microbiome. As is common in microbiome studies, when the number of variables is an order of magnitude larger than the number of samples LassoGLMM can be imperfect in its variable selection. We overcome this limitation by adding a pre-screening step to reduce the number of variables evaluated in the model. We assessed the use of this adapted two-stage LassoGLMM for its ability to determine which microbes are associated with continuous repeated clinical measures. We found associations (retaining a non-zero coefficient in the LassoGLMM) between 10 laboratory measurements and 43 bacterial genera in the oral microbiota, and between 2 cytokines and 3 bacterial genera in the lung. We compared our associations with those identified by the Wilcoxon test after dichotomizing our outcomes and identified a non-significant trend towards differential abundance between high and low outcomes. Our two-step LassoGLMM explained more of the variance seen in the outcome of interest than other variants of the LassoGLMM method. Conclusions We demonstrated a method that can account for the large number of genera detected in microbiome studies and repeated measures of clinical or longitudinal studies, allowing for the detection of strong associations between microbes and clinical measures. By incorporating the design strengths of repeated measurements and a prescreening step to aid variable selection, our two-step LassoGLMM will be a useful analytic method for investigating relationships between microbes and repeatedly measured continuous outcomes. Electronic supplementary material The online version of this article (10.1186/s13040-018-0173-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura Tipton
- 1Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 USA.,2Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003 USA
| | - Karen T Cuenco
- 3Genentech, 1 DNA Way, MS-231C, South San Francisco, CA 94080 USA.,4Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Laurence Huang
- 5Department of Medicine, School of Medicine, University of California, San Francisco, CA 94143 USA
| | - Ruth M Greenblatt
- 5Department of Medicine, School of Medicine, University of California, San Francisco, CA 94143 USA.,6Departments of Clinical Pharmacy, Epidemiology and Biostatistics, Schools of Pharmacy and Medicine, University of California, San Francisco, CA 94143 USA
| | - Eric Kleerup
- 7Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
| | - Frank Sciurba
- 8Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Steven R Duncan
- 8Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Michael P Donahoe
- 8Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Alison Morris
- 8Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213 USA
| | - Elodie Ghedin
- 1Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 USA.,2Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY 10003 USA.,9College of Global Public Health, New York University, New York, NY 10003 USA
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78
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Abstract
Studies of microbial communities have become widespread with the development of relatively inexpensive, rapid, and high throughput sequencing. However, as with all these technologies, reproducible results depend on a laboratory workflow that incorporates appropriate precautions and controls. This is particularly important with low-biomass samples where contaminating bacterial DNA can generate misleading results. This article details a semi-automated workflow to identify microbes from human breast milk samples using targeted sequencing of the 16S ribosomal RNA (rRNA) V4 region on a low- to mid-throughput scale. The protocol describes sample preparation from whole milk including: sample lysis, nucleic acid extraction, amplification of the V4 region of the 16S rRNA gene, and library preparation with quality control measures. Importantly, the protocol and discussion consider issues that are salient to the preparation and analysis of low-biomass samples including appropriate positive and negative controls, PCR inhibitor removal, sample contamination by environmental, reagent, or experimental sources, and experimental best practices designed to ensure reproducibility. While the protocol as described is specific to human milk samples, it is adaptable to numerous low- and high-biomass sample types, including samples collected on swabs, frozen neat, or stabilized in a preservation buffer.
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Affiliation(s)
- Nicole H Tobin
- Department of Pediatrics, University of California at Los Angeles
| | - Cora Woodward
- Department of Pediatrics, University of California at Los Angeles
| | - Sara Zabih
- Department of Pediatrics, University of California at Los Angeles
| | - David J Lee
- Department of Pediatrics, University of California at Los Angeles
| | - Fan Li
- Department of Pediatrics, University of California at Los Angeles
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79
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Abstract
Human microbiomes have received increasing attention over the last 10 years, leading to a pervasiveness of hypotheses relating dysbiosis to health and disease. The respiratory tract has received much less attention in this respect than that of, for example, the human gut. Nevertheless, progress has been made in elucidating the immunological, ecological and environmental drivers that govern these microbial consortia and the potential consequences of aberrant microbiomes. In this review, we consider the microbiome of the nasopharynx, a specific niche of the upper respiratory tract. The nasopharynx is an important site, anatomically with respect to its gateway position between upper and lower airways, and for pathogenic bacterial colonisation. The dynamics of the latter are important for long-term respiratory morbidity, acute infections of both invasive and non-invasive disease and associations with chronic airway disease exacerbations. Here, we review the development of the nasopharyngeal (NP) microbiome over the life course, examining it from the early establishment of resilient profiles in neonates through to perturbations associated with pneumonia risk in the elderly. We focus specifically on the commensal, opportunistically pathogenic members of the NP microbiome that includes Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae and Moraxella catarrhalis. In addition, we consider the role of relatively harmless genera such as Dolosigranulum and Corynebacterium. Understanding that the NP microbiome plays such a key, beneficial role in maintaining equilibrium of commensal species, prevention of pathogen outgrowth and host immunity enables future research to be directed appropriately.
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80
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Fraczek MG, Chishimba L, Niven RM, Bromley M, Simpson A, Smyth L, Denning DW, Bowyer P. Corticosteroid treatment is associated with increased filamentous fungal burden in allergic fungal disease. J Allergy Clin Immunol 2017; 142:407-414. [PMID: 29122659 DOI: 10.1016/j.jaci.2017.09.039] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/06/2017] [Accepted: 09/21/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND Allergic diseases caused by fungi are common. The best understood conditions are allergic bronchopulmonary aspergillosis and severe asthma with fungal sensitization. Our knowledge of the fungal microbiome (mycobiome) is limited to a few studies involving healthy individuals, asthmatics, and smokers. No study has yet examined the mycobiome in fungal lung disease. OBJECTIVES The main aim of this study was to determine the mycobiome in lungs of individuals with well-characterized fungal disease. A secondary objective was to determine possible effects of treatment on the mycobiome. METHODS After bronchoscopy, ribosomal internal transcribed spacer region 1 DNA was amplified and sequenced and fungal load determined by real-time PCR. Clinical and treatment variables were correlated with the main species identified. Bronchopulmonary aspergillosis (n = 16), severe asthma with fungal sensitization (n = 16), severe asthma not sensitized to fungi (n = 9), mild asthma patients (n = 7), and 10 healthy control subjects were studied. RESULTS The mycobiome was highly varied with severe asthmatics carrying higher loads of fungus. Healthy individuals had low fungal loads, mostly poorly characterized Malasezziales. The most common fungus in asthmatics was Aspergillus fumigatus complex and this taxon accounted for the increased burden of fungus in the high-level samples. Corticosteroid treatment was significantly associated with increased fungal load (P < .01). CONCLUSIONS The mycobiome is highly variable. Highest loads of fungus are observed in severe asthmatics and the most common fungus is Aspergillus fumigatus complex. Individuals receiving steroid therapy had significantly higher levels of Aspergillus and total fungus in their bronchoalveolar lavage.
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Affiliation(s)
- Marcin G Fraczek
- Manchester Fungal Infection Group, Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, United Kingdom; Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom; School of Biological Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Livingstone Chishimba
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom
| | - Rob M Niven
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom
| | - Mike Bromley
- Manchester Fungal Infection Group, Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Angela Simpson
- Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom
| | - Lucy Smyth
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - David W Denning
- Manchester Fungal Infection Group, Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, United Kingdom; Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom; National Aspergillosis Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom
| | - Paul Bowyer
- Manchester Fungal Infection Group, Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester, United Kingdom; Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust (Wythenshawe), Manchester, United Kingdom.
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81
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Abstract
Fungi and mammals share a co-evolutionary history and are involved in a complex web of interactions. Studies focused on commensal bacteria suggest that pathological changes in the microbiota, historically known as dysbiosis, are at the root of many inflammatory diseases of non-infectious origin. However, the importance of dysbiosis in the fungal community - the mycobiota - was only recently acknowledged to have a pathological role, as novel findings have suggested that mycobiota disruption can have detrimental effects on host immunity. Fungal dysbiosis and homeostasis are dynamic processes that are probably more common than actual fungal infections, and therefore constantly shape the immune response. In this Review, we summarize specific mycobiota patterns that are associated with fungal dysbiosis, and discuss how mucosal immunity has evolved to distinguish fungal infections from dysbiosis and how it responds to these different conditions. We propose that gut microbiota dysbiosis is a collective feature of complex interactions between prokaryotic and eukaryotic microbial communities that can affect immunity and that can influence health and disease.
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Affiliation(s)
- Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
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82
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Blander JM, Longman RS, Iliev ID, Sonnenberg GF, Artis D. Regulation of inflammation by microbiota interactions with the host. Nat Immunol 2017; 18:851-60. [PMID: 28722709 DOI: 10.1038/ni.3780] [Citation(s) in RCA: 391] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/30/2017] [Indexed: 12/13/2022]
Abstract
The study of the intestinal microbiota has begun to shift from cataloging individual members of the commensal community to understanding their contributions to the physiology of the host organism in health and disease. Here, we review the effects of the microbiome on innate and adaptive immunological players from epithelial cells and antigen-presenting cells to innate lymphoid cells and regulatory T cells. We discuss recent studies that have identified diverse microbiota-derived bioactive molecules and their effects on inflammation within the intestine and distally at sites as anatomically remote as the brain. Finally, we highlight new insights into how the microbiome influences the host response to infection, vaccination and cancer, as well as susceptibility to autoimmune and neurodegenerative disorders.
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83
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Kim D, Hofstaedter CE, Zhao C, Mattei L, Tanes C, Clarke E, Lauder A, Sherrill-Mix S, Chehoud C, Kelsen J, Conrad M, Collman RG, Baldassano R, Bushman FD, Bittinger K. Optimizing methods and dodging pitfalls in microbiome research. Microbiome 2017; 5:52. [PMID: 28476139 PMCID: PMC5420141 DOI: 10.1186/s40168-017-0267-5] [Citation(s) in RCA: 325] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/21/2017] [Indexed: 05/09/2023]
Abstract
Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors.
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Affiliation(s)
- Dorothy Kim
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Casey E. Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Erik Clarke
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Abigail Lauder
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Christel Chehoud
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Máire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
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84
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Abstract
Purpose of the review Cryptococcal disease is most often thought of in the context of HIV infection. Much of our knowledge of the disease originates from its management in the HIV-positive population over the last 30 years. While the majority of cases globally continue to occur in the setting of advanced HIV, Cryptococcus species is increasingly responsible for disease in HIV-negative populations including those considered normal hosts and these HIV-negative populations will be the focus of this review. Recent findings Currently available data indicated that significant differences exist in epidemiology, clinical presentation, management and outcomes of cryptococcal disease in HIV-negative populations when compared to those living with HIV. Summary Further research is required to improve our knowledge of cryptococcal disease in particular in HIV-negative cohorts so as to optimise management of the disease in the future.
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85
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Millares L, Bermudo G, Pérez-Brocal V, Domingo C, Garcia-Nuñez M, Pomares X, Moya A, Monsó E. The respiratory microbiome in bronchial mucosa and secretions from severe IgE-mediated asthma patients. BMC Microbiol 2017; 17:20. [PMID: 28103814 PMCID: PMC5248442 DOI: 10.1186/s12866-017-0933-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/13/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The bronchial microbiome in chronic lung diseases presents an abnormal pattern, but its microbial composition and regional differences in severe asthma have not been sufficiently addressed. The aim of the study was to describe the bacterial community in bronchial mucosa and secretions of patients with severe chronic asthma chronically treated with corticosteroids in addition to usual care according to Global Initiative for Asthma. Bacterial community composition was obtained by 16S rRNA gene amplification and sequencing, and functional capabilities through PICRUSt. RESULTS Thirteen patients with severe asthma were included and provided 11 bronchial biopsies (BB) and 12 bronchial aspirates (BA) suitable for sequence analyses. Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria showed relative abundances (RAs) over 5% in BB, a cutoff that was reached by Streptococcus and Prevotella at genus level. Legionella genus attained a median RA of 2.7 (interquartile range 1.1-4.7) in BB samples. In BA a higher RA of Fusobacteria was found, when compared with BB [8.7 (5.9-11.4) vs 4.2 (0.8-7.5), p = 0.037], while the RA of Proteobacteria was lower in BA [4.3 (3.7-6.5) vs 17.1 (11.2-33.4), p = 0.005]. RA of the Legionella genus was also significantly lower in BA [0.004 (0.001-0.02) vs. 2.7 (1.1-4.7), p = 0.005]. Beta-diversity analysis confirmed the differences between the microbial communities in BA and BB (R2 = 0.20, p = 0.001, Adonis test), and functional analysis revealed also statistically significant differences between both types of sample on Metabolism, Cellular processes, Human diseases, Organismal systems and Genetic information processing pathways. CONCLUSIONS The microbiota in the bronchial mucosa of severe asthma has a specific pattern that is not accurately represented in bronchial secretions, which must be considered a different niche of bacteria growth.
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Affiliation(s)
- Laura Millares
- Fundació Parc Taulí, Parc Taulí 1, Edificio Santa Fe, planta baja, 08208, Sabadell, Barcelona, Spain.
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid, Spain.
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain.
- Fundació Insitut d'Investigació Germans Trias i Pujol, Badalona, Spain.
| | - Guadalupe Bermudo
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Vicente Pérez-Brocal
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Evolutionary Genetics Unit, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Christian Domingo
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Marian Garcia-Nuñez
- Fundació Parc Taulí, Parc Taulí 1, Edificio Santa Fe, planta baja, 08208, Sabadell, Barcelona, Spain
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Fundació Insitut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Xavier Pomares
- Department of Respiratory Medicine, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Andrés Moya
- Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Evolutionary Genetics Unit, Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Valencia, Spain
| | - Eduard Monsó
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid, Spain
- Universitat Autònoma de Barcelona, Esfera UAB, Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
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86
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Krause R, Moissl-Eichinger C, Halwachs B, Gorkiewicz G, Berg G, Valentin T, Prattes J, Högenauer C, Zollner-Schwetz I. Mycobiome in the Lower Respiratory Tract - A Clinical Perspective. Front Microbiol 2017; 7:2169. [PMID: 28119685 PMCID: PMC5222816 DOI: 10.3389/fmicb.2016.02169] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/23/2016] [Indexed: 01/01/2023] Open
Abstract
Recently the paradigm that the healthy lung is sterile was challenged and it is now believed that the lungs harbor a diverse microbiota also contributing to the pathogenesis of various diseases. Most of the research studies targeting the respiratory microbiome have focused on bacteria and their impact on lung health and lung diseases. Recently, also the mycobiome has gained attention. Lower respiratory tract (LRT) diseases (e.g., cystic fibrosis) and other diseases or conditions (e.g., HIV infection, lung transplantation, and treatment at intensive care units) have been investigated with regard to possible involvement of mycobiome in development or progression of diseases. It has been shown that diversities of mycobiome in the LRT vary in different populations and conditions. It has been proposed that the mycobiome diversity associated with LRT can vary with different stages of diseases. Overall, Candida was the dominant fungal genus in LRT samples. In this review, we summarize the recent findings regarding the human LRT mycobiome from a clinical perspective focussing on characterization of investigated patient groups and healthy controls as well as sampling techniques. From these data, clinical implications for further studies or routine practice are drawn. To obtain clinically relevant answers efforts should be enhanced to collect well characterized and described patient groups as well as healthy individuals for comparative data analysis and to apply thorough sampling techniques. We need to proceed with elucidation of the role of mycobiota in healthy LRT and LRT diseases to hopefully improve patient care.
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Affiliation(s)
- Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz Graz, Austria
| | - Christine Moissl-Eichinger
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of GrazGraz, Austria; BioTechMed, Medical University of GrazGraz, Austria
| | - Bettina Halwachs
- Institute of Pathology, Medical University of Graz Graz, Austria
| | - Gregor Gorkiewicz
- BioTechMed, Medical University of GrazGraz, Austria; Institute of Pathology, Medical University of GrazGraz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
| | - Thomas Valentin
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz Graz, Austria
| | - Jürgen Prattes
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz Graz, Austria
| | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz Graz, Austria
| | - Ines Zollner-Schwetz
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz Graz, Austria
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87
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Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, Küsel K, Rillig MC, Rivett DW, Salles JF, van der Heijden MG, Youssef NH, Zhang X, Wei Z, Hol WH. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J 2017; 11:853-62. [PMID: 28072420 DOI: 10.1038/ismej.2016.174] [Citation(s) in RCA: 525] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 11/06/2016] [Accepted: 11/12/2016] [Indexed: 02/05/2023]
Abstract
Rare species are increasingly recognized as crucial, yet vulnerable components of Earth's ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning. We discuss how rare species can have a preponderant role for local biodiversity and species turnover with rarity potentially bound to phylogenetically conserved features. Rare microbes may therefore be overlooked keystone species regulating the functioning of host-associated, terrestrial and aquatic environments. We conclude this review with recommendations to guide scientists interested in investigating this rapidly emerging research area.
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88
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Abstract
The fungi that reside in the human lungs represent an understudied, but medically relevant comm-unity. From the few studies published on the lung mycobiome, we find that there are fungi in both the healthy and diseased respiratory tract, that these fungi vary widely between individuals, and that there is a trend toward lower fungal diversity among individuals with disease. This review discusses the few studies of the lung mycobiome and details the challenges that accompany lung mycobiome studies. These challenges include sample collection and processing, sequence amplification and processing, and a history of multiple names for species. Some challenges may never be solved, but others can be solved with more data and additional studies of the lung mycobiome.
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Affiliation(s)
- Laura Tipton
- a Department of Computational and Systems Biology , University of Pittsburgh School of Medicine , Pittsburgh , PA , USA.,b Department of Biology , New York University , New York , NY , USA
| | - Elodie Ghedin
- b Department of Biology , New York University , New York , NY , USA
| | - Alison Morris
- c Departments of Medicine and Immunology , University of Pittsburgh School of Medicine , Pittsburgh , PA , USA
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89
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Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD. Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Cell Host Microbe 2016; 18:489-500. [PMID: 26468751 DOI: 10.1016/j.chom.2015.09.008] [Citation(s) in RCA: 514] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/31/2015] [Accepted: 09/22/2015] [Indexed: 12/13/2022]
Abstract
Abnormal composition of intestinal bacteria--"dysbiosis"-is characteristic of Crohn's disease. Disease treatments include dietary changes and immunosuppressive anti-TNFα antibodies as well as ancillary antibiotic therapy, but their effects on microbiota composition are undetermined. Using shotgun metagenomic sequencing, we analyzed fecal samples from a prospective cohort of pediatric Crohn's disease patients starting therapy with enteral nutrition or anti-TNFα antibodies and reveal the full complement and dynamics of bacteria, fungi, archaea, and viruses during treatment. Bacterial community membership was associated independently with intestinal inflammation, antibiotic use, and therapy. Antibiotic exposure was associated with increased dysbiosis, whereas dysbiosis decreased with reduced intestinal inflammation. Fungal proportions increased with disease and antibiotic use. Dietary therapy had independent and rapid effects on microbiota composition distinct from other stressor-induced changes and effectively reduced inflammation. These findings reveal that dysbiosis results from independent effects of inflammation, diet, and antibiotics and shed light on Crohn disease treatments.
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Affiliation(s)
- James D Lewis
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric Z Chen
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert N Baldassano
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anthony R Otley
- Department of Pediatrics, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Anne M Griffiths
- Division of Gastroenterology Hepatology and Nutrition, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Dale Lee
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Pediatric Gastroenterology Hepatology and Nutrition, Seattle Children's Hospital, University of Washington, Seattle, WA 98105, USA
| | - Kyle Bittinger
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aubrey Bailey
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elliot S Friedman
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christian Hoffmann
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lindsey Albenberg
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Rohini Sinha
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlene Compher
- School of Nursing, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin Gilroy
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lisa Nessel
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amy Grant
- Department of Pediatrics, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Christel Chehoud
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongzhe Li
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gary D Wu
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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90
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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91
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Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, Bittinger K, Leite R, Elovitz MA, Parry S, Bushman FD. Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome 2016; 4:29. [PMID: 27338728 PMCID: PMC4917942 DOI: 10.1186/s40168-016-0172-3] [Citation(s) in RCA: 350] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/30/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Recent studies have suggested that bacteria associated with the placenta-a "placental microbiome"-may be important in reproductive health and disease. However, a challenge in working with specimens with low bacterial biomass, such as placental samples, is that some or all of the bacterial DNA may derive from contamination in dust or commercial reagents. To investigate this, we compared placental samples from healthy deliveries to a matched set of contamination controls, as well as to oral and vaginal samples from the same women. RESULTS We quantified total 16S rRNA gene copies using quantitative PCR and found that placental samples and negative controls contained low and indistinguishable copy numbers. Oral and vaginal swab samples, in contrast, showed higher copy numbers. We carried out 16S rRNA gene sequencing and community analysis and found no separation between communities from placental samples and contamination controls, though oral and vaginal samples showed characteristic, distinctive composition. Two different DNA purification methods were compared with similar conclusions, though the composition of the contamination background differed. Authentically present microbiota should yield mostly similar results regardless of the purification method used-this was seen for oral samples, but no placental bacterial lineages were (1) shared between extraction methods, (2) present at >1 % of the total, and (3) present at greater abundance in placental samples than contamination controls. CONCLUSIONS We conclude that for this sample set, using the methods described, we could not distinguish between placental samples and contamination introduced during DNA purification.
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Affiliation(s)
- Abigail P Lauder
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Aoife M Roche
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Aubrey Bailey
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Alice L Laughlin
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Kyle Bittinger
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA
| | - Rita Leite
- Department of Obstetrics and Gynecology, Maternal and Child Health Research Program, Perelman School of Medicine at the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA, 19104, USA
| | - Michal A Elovitz
- Department of Obstetrics and Gynecology, Maternal and Child Health Research Program, Perelman School of Medicine at the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA, 19104, USA
| | - Samuel Parry
- Department of Obstetrics and Gynecology, Maternal and Child Health Research Program, Perelman School of Medicine at the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA, 19104, USA.
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104-6076, USA.
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92
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Imabayashi Y, Moriyama M, Takeshita T, Ieda S, Hayashida JN, Tanaka A, Maehara T, Furukawa S, Ohta M, Kubota K, Yamauchi M, Ishiguro N, Yamashita Y, Nakamura S. Molecular analysis of fungal populations in patients with oral candidiasis using next-generation sequencing. Sci Rep 2016; 6:28110. [PMID: 27305838 DOI: 10.1038/srep28110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/31/2016] [Indexed: 01/06/2023] Open
Abstract
Oral candidiasis is closely associated with changes in oral fungal biodiversity and is caused primarily by Candida albicans. However, the widespread use of empiric and prophylactic antifungal drugs has caused a shift in fungal biodiversity towards other Candida or yeast species. Recently, next-generation sequencing (NGS) has provided an improvement over conventional culture techniques, allowing rapid comprehensive analysis of oral fungal biodiversity. In this study, we used NGS to examine the oral fungal biodiversity of 27 patients with pseudomembranous oral candidiasis (POC) and 66 healthy controls. The total number of fungal species in patients with POC and healthy controls was 67 and 86, respectively. The copy number of total PCR products and the proportion of non-C. albicans, especially C. dubliniensis, in patients with POC, were higher than those in healthy controls. The detection patterns in patients with POC were similar to those in controls after antifungal treatment. Interestingly, the number of fungal species and the copy number of total PCR products in healthy controls increased with aging. These results suggest that high fungal biodiversity and aging might be involved in the pathogenesis of oral candidiasis. We therefore conclude that NGS is a useful technique for investigating oral candida infections.
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93
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Krause R, Halwachs B, Thallinger GG, Klymiuk I, Gorkiewicz G, Hoenigl M, Prattes J, Valentin T, Heidrich K, Buzina W, Salzer HJF, Rabensteiner J, Prüller F, Raggam RB, Meinitzer A, Moissl-Eichinger C, Högenauer C, Quehenberger F, Kashofer K, Zollner-Schwetz I. Characterisation of Candida within the Mycobiome/Microbiome of the Lower Respiratory Tract of ICU Patients. PLoS One 2016; 11:e0155033. [PMID: 27206014 PMCID: PMC4874575 DOI: 10.1371/journal.pone.0155033] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/22/2016] [Indexed: 02/06/2023] Open
Abstract
Whether the presence of Candida spp. in lower respiratory tract (LRT) secretions is a marker of underlying disease, intensive care unit (ICU) treatment and antibiotic therapy or contributes to poor clinical outcome is unclear. We investigated healthy controls, patients with proposed risk factors for Candida growth in LRT (antibiotic therapy, ICU treatment with and without antibiotic therapy), ICU patients with pneumonia and antibiotic therapy and candidemic patients (for comparison of truly invasive and colonizing Candida spp.). Fungal patterns were determined by conventional culture based microbiology combined with molecular approaches (next generation sequencing, multilocus sequence typing) for description of fungal and concommitant bacterial microbiota in LRT, and host and fungal biomarkes were investigated. Admission to and treatment on ICUs shifted LRT fungal microbiota to Candida spp. dominated fungal profiles but antibiotic therapy did not. Compared to controls, Candida was part of fungal microbiota in LRT of ICU patients without pneumonia with and without antibiotic therapy (63% and 50% of total fungal genera) and of ICU patients with pneumonia with antibiotic therapy (73%) (p<0.05). No case of invasive candidiasis originating from Candida in the LRT was detected. There was no common bacterial microbiota profile associated or dissociated with Candida spp. in LRT. Colonizing and invasive Candida strains (from candidemic patients) did not match to certain clades withdrawing the presence of a particular pathogenic and invasive clade. The presence of Candida spp. in the LRT rather reflected rapidly occurring LRT dysbiosis driven by ICU related factors than was associated with invasive candidiasis.
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Affiliation(s)
- Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- * E-mail:
| | - Bettina Halwachs
- Bioinformatics, Institute for Knowledge Discovery, University of Technology, Graz, Austria and OMICS Center Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | | | - Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | | | - Martin Hoenigl
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Jürgen Prattes
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Thomas Valentin
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Katharina Heidrich
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Department of Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Walter Buzina
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Helmut J. F. Salzer
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibnitz Center for Medicine and Biosciences, Borstel, Germany
| | - Jasmin Rabensteiner
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Florian Prüller
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Reinhard B. Raggam
- Division of Angiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Andreas Meinitzer
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Christoph Högenauer
- Theodor Escherich Laboratory for Microbiome Research, Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Franz Quehenberger
- Institute for Medical Informatics, Statistics, and Documentation, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Ines Zollner-Schwetz
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
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94
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Abstract
New state-of-the-art techniques in sequencing offer valuable tools in both detection of mycobiota and in understanding of the molecular mechanisms of resistance against antifungal compounds and virulence. Introduction of new sequencing platform with enhanced capacity and a reduction in costs for sequence analysis provides a potential powerful tool in mycological diagnosis and research. In this review, we summarize the applications of next-generation sequencing techniques in mycology.
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95
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Stefanini I, Albanese D, Cavazza A, Franciosi E, De Filippo C, Donati C, Cavalieri D. Dynamic changes in microbiota and mycobiota during spontaneous 'Vino Santo Trentino' fermentation. Microb Biotechnol 2016; 9:195-208. [PMID: 26780037 PMCID: PMC4767281 DOI: 10.1111/1751-7915.12337] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/19/2015] [Accepted: 10/28/2015] [Indexed: 02/03/2023] Open
Abstract
Vino Santo is a sweet wine produced from late harvesting and pressing of Nosiola grapes in a small, well-defined geographical area in the Italian Alps. We used metagenomics to characterize the dynamics of microbial communities in the products of three wineries, resulting from spontaneous fermentation with almost the same timing and procedure. Comparing fermentation dynamics and grape microbial composition, we show a rapid increase in a small number of wine yeast species, with a parallel decrease in complexity. Despite the application of similar protocols, slight changes in the procedures led to significant differences in the microbiota in the three cases of fermentation: (i) fungal content of the must varied significantly in the different wineries, (ii) Pichia membranifaciens persisted in only one of the wineries, (iii) one fermentation was characterized by the balanced presence of Saccharomyces cerevisiae and Hanseniaspora osmophila during the later phases. We suggest the existence of a highly winery-specific 'microbial-terroir' contributing significantly to the final product rather than a regional 'terroir'. Analysis of changes in abundance during fermentation showed evident correlations between different species, suggesting that fermentation is the result of a continuum of interaction between different species and physical-chemical parameters.
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Affiliation(s)
- Irene Stefanini
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Davide Albanese
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Agostino Cavazza
- Food Quality Nutrition & Health Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Elena Franciosi
- Food Quality Nutrition & Health Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Carlotta De Filippo
- Food Quality Nutrition & Health Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.,Institute of Biometeorology - IBIMET, National Research Council, Florence, Italy
| | - Claudio Donati
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Duccio Cavalieri
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.,Institute of Biometeorology - IBIMET, National Research Council, Florence, Italy.,Department of Biology, University of Florence, Florence, Italy
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96
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Alifirova VM, Zhukova NG, Zhukova IA, Latypova AV, Titova MA, Mironova YS, Izhboldina OP, Nikitina MA, Petrov VA. [A role of the gastrointestinal tract microbiota in the pathogenesis of Parkinson's disease]. Zh Nevrol Psikhiatr Im S S Korsakova 2016. [PMID: 28635757 DOI: 10.17116/jnevro2016116111174-179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Microbiota is a community of microorganisms, viruses, protozoa, colonizing the gut. There are tight phylogenetic relationships between the gut microbiota and the human body, the disturbance of which may lead to the CNS dysfunction as well as to the development of neurodegenerative diseases. This review focuses on general and specific aspects of the influence of gut microbiota on the pathogenesis of Parkinson's disease (PD). Current theories and models of the relationship between microbiota and brain structures in PD are presented with a specific focus on neurochemical and immunological aspects of the problem.
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Affiliation(s)
| | - N G Zhukova
- Siberian State Medical University, Tomsk, Russia
| | - I A Zhukova
- Siberian State Medical University, Tomsk, Russia
| | - A V Latypova
- Siberian State Medical University, Tomsk, Russia
| | - M A Titova
- Siberian State Medical University, Tomsk, Russia
| | | | | | - M A Nikitina
- Siberian State Medical University, Tomsk, Russia
| | - V A Petrov
- Siberian State Medical University, Tomsk, Russia
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97
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Lee S, Yamamoto N. Accuracy of the high-throughput amplicon sequencing to identify species within the genus Aspergillus. Fungal Biol 2015; 119:1311-1321. [PMID: 26615752 DOI: 10.1016/j.funbio.2015.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/24/2015] [Accepted: 10/07/2015] [Indexed: 11/28/2022]
Abstract
This study characterized the accuracy of high-throughput amplicon sequencing to identify species within the genus Aspergillus. To this end, we sequenced the internal transcribed spacer 1 (ITS1), β-tubulin (BenA), and calmodulin (CaM) gene encoding sequences as DNA markers from eight reference Aspergillus strains with known identities using 300-bp sequencing on the Illumina MiSeq platform, and compared them with the BLASTn outputs. The identifications with the sequences longer than 250 bp were accurate at the section rank, with some ambiguities observed at the species rank due to mostly cross detection of sibling species. Additionally, in silico analysis was performed to predict the identification accuracy for all species in the genus Aspergillus, where 107, 210, and 187 species were predicted to be identifiable down to the species rank based on ITS1, BenA, and CaM, respectively. Finally, air filter samples were analysed to quantify the relative abundances of Aspergillus species in outdoor air. The results were reproducible across biological duplicates both at the species and section ranks, but not strongly correlated between ITS1 and BenA, suggesting the Aspergillus detection can be taxonomically biased depending on the selection of the DNA markers and/or primers.
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Affiliation(s)
- Seungeun Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 151-742, South Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 151-742, South Korea.
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98
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99
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Chehoud C, Albenberg LG, Judge C, Hoffmann C, Grunberg S, Bittinger K, Baldassano RN, Lewis JD, Bushman FD, Wu GD. Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease. Inflamm Bowel Dis 2015; 21:1948-56. [PMID: 26083617 DOI: 10.1097/MIB.0000000000000454] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) involves dysregulation of mucosal immunity in response to environmental factors such as the gut microbiota. The bacterial microbiota is often altered in IBD, but the connection to disease is not fully clarified and gut fungi have recently been suggested to play a role as well. In this study, we compared microbes from all 3 domains of life-bacteria, archaea, and eukaryota-in pediatric patients with IBD and healthy controls. METHODS A stool sample was collected from patients with IBD (n = 32) or healthy control subjects (n = 90), and bacterial, archaeal, and fungal communities were characterized by deep sequencing of rRNA gene segments specific to each domain. RESULTS Patients with IBD (Crohn's disease or ulcerative colitis) had lower bacterial diversity and distinctive fungal communities. Two lineages annotating as Candida were significantly more abundant in patients with IBD (P = 0.0034 and P = 0.00038, respectively), whereas a lineage annotating as Cladosporium was more abundant in healthy subjects (P = 0.0025). There were no statistically significant differences in archaea, which were rare in pediatric samples compared with those from adults. CONCLUSIONS Pediatric IBD is associated with reduced diversity in both fungal and bacterial gut microbiota. Specific Candida taxa were found to be increased in abundance in the IBD samples. These data emphasize the potential importance of fungal microbiota signatures as biomarkers of pediatric IBD, supporting their possible role in disease pathogenesis.
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100
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Affiliation(s)
- Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
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