51
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Marsh RL, Nelson MT, Pope CE, Leach AJ, Hoffman LR, Chang AB, Smith-Vaughan HC. How low can we go? The implications of low bacterial load in respiratory microbiota studies. Pneumonia (Nathan) 2018; 10:7. [PMID: 30003009 PMCID: PMC6033291 DOI: 10.1186/s41479-018-0051-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022] Open
Abstract
Background Culture-independent sequencing methods are increasingly used to investigate the microbiota associated with human mucosal surfaces, including sites that have low bacterial load in healthy individuals (e.g. the lungs). Standard microbiota methods developed for analysis of high bacterial load specimens (e.g. stool) may require modification when bacterial load is low, as background contamination derived from sterile laboratory reagents and kits can dominate sequence data when few bacteria are present. Main body Bacterial load in respiratory specimens may vary depending on the specimen type, specimen volume, the anatomic site sampled and clinical parameters. This review discusses methodological issues inherent to analysis of low bacterial load specimens and recommends strategies for successful respiratory microbiota studies. The range of methods currently used to process DNA from low bacterial load specimens, and the strategies used to identify and exclude background contamination are also discussed. Conclusion Microbiota studies that include low bacterial load specimens require additional tests to ensure that background contamination does not bias the results or interpretation. Several methods are currently used to analyse the microbiota in low bacterial load respiratory specimens; however, there is scant literature comparing the effectiveness and biases of different methods. Further research is needed to define optimal methods for analysing the microbiota in low bacterial load specimens.
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Affiliation(s)
- Robyn L Marsh
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
| | - Maria T Nelson
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Chris E Pope
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Amanda J Leach
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
| | - Lucas R Hoffman
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Anne B Chang
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia.,3Department of Respiratory and Sleep Medicine, Children's Health Queensland and Queensland University of Technology, Brisbane, QLD Australia
| | - Heidi C Smith-Vaughan
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
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52
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Mika M, Nita I, Morf L, Qi W, Beyeler S, Bernasconi E, Marsland BJ, Ott SR, von Garnier C, Hilty M. Microbial and host immune factors as drivers of COPD. ERJ Open Res 2018; 4:00015-2018. [PMID: 29992131 PMCID: PMC6028745 DOI: 10.1183/23120541.00015-2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/28/2018] [Indexed: 12/29/2022] Open
Abstract
Compartmentalisation of the respiratory tract microbiota in patients with different chronic obstructive pulmonary disease (COPD) severity degrees needs to be systematically investigated. In addition, it is unknown if the inflammatory and emphysematous milieux in patients with COPD are associated with changes in the respiratory tract microbiota and host macrophage gene expression. We performed a cross-sectional study to compare non-COPD controls (n=10) to COPD patients (n=32) with different disease severity degrees. Samples (n=187) were obtained from different sites of the upper and lower respiratory tract. Microbiota analyses were performed by 16S ribosomal RNA gene sequencing and host gene expression analyses by quantitative real-time PCR of distinct markers of bronchoalveolar lavage cells. Overall, the microbial communities of severe COPD (Global Initiative for Chronic Obstructive Lung Disease (GOLD) grade 3/4) patients clustered significantly differently to controls and less severe COPD (GOLD 1/2) patients (permutational multivariate ANOVA (MANOVA), p=0.001). However, we could not detect significant associations between the different sampling sites in the lower airways. In addition, the chosen set of host gene expression markers significantly separated COPD GOLD 3/4 patients, and we found correlations between the composition of the microbiota and the host data. In conclusion, this study demonstrates associations between host gene expression and microbiota profiles that may influence the course of COPD. Associations of the host immune response and a disordered microbiota in patients with different COPD severity degreeshttp://ow.ly/h2mW30k9Nua
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Affiliation(s)
- Moana Mika
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern Switzerland
| | - Izabela Nita
- Pulmonary Medicine Laboratory, Dept of Biomedical Research, University of Bern, Bern, Switzerland
| | - Laura Morf
- Pulmonary Medicine Laboratory, Dept of Biomedical Research, University of Bern, Bern, Switzerland
| | - Weihong Qi
- Functional Genomics Center, Swiss Federal Institute of Technology Zurich/University of Zurich, Zurich, Switzerland
| | - Seraina Beyeler
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern Switzerland.,Pulmonary Medicine Laboratory, Dept of Biomedical Research, University of Bern, Bern, Switzerland
| | - Eric Bernasconi
- Service de Pneumologie, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Benjamin J Marsland
- Service de Pneumologie, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Sebastian R Ott
- Dept of Pulmonary Medicine, Bern University Hospital, Inselspital, Bern, Switzerland
| | - Christophe von Garnier
- Pulmonary Medicine Laboratory, Dept of Biomedical Research, University of Bern, Bern, Switzerland.,Dept of Pulmonary Medicine, Bern University Hospital, Inselspital, Bern, Switzerland.,These authors contributed equally
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland.,These authors contributed equally
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53
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Microbiota Composition in Upper Respiratory Tracts of Healthy Children in Shenzhen, China, Differed with Respiratory Sites and Ages. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6515670. [PMID: 30013985 PMCID: PMC6022278 DOI: 10.1155/2018/6515670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/07/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022]
Abstract
The upper respiratory tract (URT) is home to various microbial commensals, which function as competitors to pathogens and help train the immune system. However, few studies have reported the normal microbiota carriage in the URT of healthy Chinese children. In this study, we performed a 16S rDNA gene sequencing analysis of 83 anterior nares (ANs), 60 nasopharynx (NP), and 97 oropharynx (OP) samples from 98 healthy children in Shenzhen, China (≤12 years of age). The microbiota in ANs and NP is the same at different ages and typical species in these sites include Moraxella, Staphylococcus, Corynebacterium, Streptococcus, and Dolosigranulum. By contrast, the OP is primarily colonized by Streptococcus, Prevotella, Neisseria, Veillonella, Rothia, Leptotrichia, and Haemophilus. Streptococcus and Rothia keep low abundance in OP microbiota of children ≤1 year old, whereas Prevotella, Neisseria, Haemophilus, and Leptotrichia amass significantly in individuals >1 year old. This work furnishes an important reference for understanding microbial dysbiosis in the URT of Chinese paediatric patients.
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54
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Hakansson AP, Orihuela CJ, Bogaert D. Bacterial-Host Interactions: Physiology and Pathophysiology of Respiratory Infection. Physiol Rev 2018; 98:781-811. [PMID: 29488821 PMCID: PMC5966719 DOI: 10.1152/physrev.00040.2016] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023] Open
Abstract
It has long been thought that respiratory infections are the direct result of acquisition of pathogenic viruses or bacteria, followed by their overgrowth, dissemination, and in some instances tissue invasion. In the last decades, it has become apparent that in contrast to this classical view, the majority of microorganisms associated with respiratory infections and inflammation are actually common members of the respiratory ecosystem and only in rare circumstances do they cause disease. This suggests that a complex interplay between host, environment, and properties of colonizing microorganisms together determines disease development and its severity. To understand the pathophysiological processes that underlie respiratory infectious diseases, it is therefore necessary to understand the host-bacterial interactions occurring at mucosal surfaces, along with the microbes inhabiting them, during symbiosis. Current knowledge regarding host-bacterial interactions during asymptomatic colonization will be discussed, including a plausible role for the human microbiome in maintaining a healthy state. With this as a starting point, we will discuss possible disruptive factors contributing to dysbiosis, which is likely to be a key trigger for pathobionts in the development and pathophysiology of respiratory diseases. Finally, from this renewed perspective, we will reflect on current and potential new approaches for treatment in the future.
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Affiliation(s)
- A P Hakansson
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University , Lund , Sweden ; Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama ; and Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh , Edinburgh , United Kingdom
| | - C J Orihuela
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University , Lund , Sweden ; Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama ; and Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh , Edinburgh , United Kingdom
| | - D Bogaert
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University , Lund , Sweden ; Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama ; and Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh , Edinburgh , United Kingdom
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55
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Nasher F, Heller M, Hathaway LJ. Streptococcus pneumoniae Proteins AmiA, AliA, and AliB Bind Peptides Found in Ribosomal Proteins of Other Bacterial Species. Front Microbiol 2018; 8:2688. [PMID: 29379482 PMCID: PMC5775242 DOI: 10.3389/fmicb.2017.02688] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/26/2017] [Indexed: 11/13/2022] Open
Abstract
The nasopharynx is frequently colonized by both commensal and pathogenic bacteria including Streptococcus pneumoniae (pneumococcus). Pneumococcus is an important pathogen responsible for bacterial meningitis and community acquired pneumonia but is also commonly an asymptomatic colonizer of the nasopharynx. Understanding interactions between microbes may provide insights into pathogenesis. Here, we investigated the ability of the three oligopeptide-binding proteins AmiA, AliA, and AliB of an ATP-binding cassette transporter of pneumococcus to detect short peptides found in other bacterial species. We found three possible peptide ligands for AmiA and four each for AliA and AliB of which two for each protein matched ribosomal proteins of other bacterial species. Using synthetic peptides we confirmed the following binding: AmiA binds peptide AKTIKITQTR, matching 50S ribosomal subunit protein L30, AliA binds peptide FNEMQPIVDRQ, matching 30S ribosomal protein S20, and AliB binds peptide AIQSEKARKHN, matching 30S ribosomal protein S20, without excluding the possibility of binding of the other peptides. These Ami-AliA/AliB peptide ligands are found in multiple species in the class of Gammaproteobacteria which includes common colonizers of the nostrils and nasopharynx. Binding such peptides may enable pneumococcus to detect and respond to neighboring species in its environment and is a potential mechanism for interspecies communication and environmental surveillance.
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Affiliation(s)
- Fauzy Nasher
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Manfred Heller
- Department of Clinical Research, Proteomics and Mass Spectrometry Core Facility, University of Bern, Bern, Switzerland
| | - Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
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56
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Bomar L, Brugger SD, Lemon KP. Bacterial microbiota of the nasal passages across the span of human life. Curr Opin Microbiol 2017; 41:8-14. [PMID: 29156371 DOI: 10.1016/j.mib.2017.10.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/15/2023]
Abstract
The human nasal passages host major human pathogens. Recent research suggests that the microbial communities inhabiting the epithelial surfaces of the nasal passages are a key factor in maintaining a healthy microenvironment by affecting both resistance to pathogens and immunological responses. The nasal bacterial microbiota shows distinct changes over the span of human life and disruption by environmental factors might be associated with both short- and long-term health consequences, such as susceptibility to viral and bacterial infections and disturbances of the immunological balance. Because infants and older adults experience a high burden of morbidity and mortality from respiratory tract infections, we review recent data on the bacterial nasal microbiota composition in health and acute respiratory infection in these age groups.
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Affiliation(s)
- Lindsey Bomar
- The Forsyth Institute (Microbiology), Cambridge, MA, United States; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, United States
| | - Silvio D Brugger
- The Forsyth Institute (Microbiology), Cambridge, MA, United States; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, United States
| | - Katherine P Lemon
- The Forsyth Institute (Microbiology), Cambridge, MA, United States; Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States.
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57
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Sakwinska O, Foata F, Berger B, Brüssow H, Combremont S, Mercenier A, Dogra S, Soh SE, Yen JCK, Heong GYS, Lee YS, Yap F, Meaney MJ, Chong YS, Godfrey KM, Holbrook JD. Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose? Benef Microbes 2017; 8:763-778. [PMID: 29022384 DOI: 10.3920/bm2017.0064] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The acquisition and early maturation of infant microbiota is not well understood despite its likely influence on later health. We investigated the contribution of the maternal microbiota to the microbiota of infant gut and nose in the context of mode of delivery and feeding. Using 16S rRNA sequencing and specific qPCR, we profiled microbiota of 42 mother-infant pairs from the GUSTO birth cohort, at body sites including maternal vagina, rectum and skin; and infant stool and nose. In our study, overlap between maternal vaginal microbiota and infant faecal microbiota was minimal, while the similarity between maternal rectal microbiota and infant microbiota was more pronounced. However, an infant's nasal and gut microbiota were no more similar to that of its own mother, than to that of unrelated mothers. These findings were independent of delivery mode. We conclude that the transfer of maternal vaginal microbes play a minor role in seeding infant stool microbiota. Transfer of maternal rectal microbiota could play a larger role in seeding infant stool microbiota, but approaches other than the generally used analyses of community similarity measures are likely to be needed to quantify bacterial transmission. We confirmed the clear difference between microbiota of infants born by Caesarean section compared to vaginally delivered infants and the impact of feeding mode on infant gut microbiota. Only vaginally delivered, fully breastfed infants had gut microbiota dominated by Bifidobacteria. Our data suggest that reduced transfer of maternal vaginal microbial is not the main mechanism underlying the differential infant microbiota composition associated with Caesarean delivery. The sources of a large proportion of infant microbiota could not be identified in maternal microbiota, and the sources of seeding of infant gut and nasal microbiota remain to be elucidated.
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Affiliation(s)
- O Sakwinska
- 1 Nestlé Research Center, Vers-Chez-Les-Blanc, 1000 Lausanne, Switzerland
| | - F Foata
- 1 Nestlé Research Center, Vers-Chez-Les-Blanc, 1000 Lausanne, Switzerland
| | - B Berger
- 1 Nestlé Research Center, Vers-Chez-Les-Blanc, 1000 Lausanne, Switzerland
| | - H Brüssow
- 1 Nestlé Research Center, Vers-Chez-Les-Blanc, 1000 Lausanne, Switzerland
| | - S Combremont
- 1 Nestlé Research Center, Vers-Chez-Les-Blanc, 1000 Lausanne, Switzerland
| | - A Mercenier
- 1 Nestlé Research Center, Vers-Chez-Les-Blanc, 1000 Lausanne, Switzerland
| | - S Dogra
- 2 Singapore Institute for Clinical Sciences (SICS), Agency for Science and Technology Research (A*STAR), 30 Medical Drive, 117609 Singapore.,3 Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, 119228 Singapore
| | - S-E Soh
- 2 Singapore Institute for Clinical Sciences (SICS), Agency for Science and Technology Research (A*STAR), 30 Medical Drive, 117609 Singapore.,4 Vishuo BioMedical Pte Ltd, 03-33/35A, Teletech Park, 2O Science Park Road, Singapore
| | - J C K Yen
- 5 Department of Reproductive Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, 229899 Singapore
| | - G Y S Heong
- 6 Department of Maternal Fetal Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, 229899 Singapore.,7 Duke-NUS Medical School, 8 College Road, 169857 Singapore.,8 Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 1E Kent Ridge Road, 119228 Singapore
| | - Y S Lee
- 2 Singapore Institute for Clinical Sciences (SICS), Agency for Science and Technology Research (A*STAR), 30 Medical Drive, 117609 Singapore.,3 Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, 119228 Singapore.,9 Division of Paediatric Endocrinology and Diabetes, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, 1E Kent Ridge Road, 119228 Singapore
| | - F Yap
- 10 Department of Paediatric Endocrinology, KK Women's and Children's Hospital, 100 Bukit Timah Road, 229899 Singapore
| | - M J Meaney
- 2 Singapore Institute for Clinical Sciences (SICS), Agency for Science and Technology Research (A*STAR), 30 Medical Drive, 117609 Singapore.,11 Ludmer Centre for Neuroinformatics and Mental Health, Douglas University Mental Health Institute, McGill University, 3755 Côte-Ste-Catherine Montreal, QC H3T 1E2 Canada
| | - Y-S Chong
- 2 Singapore Institute for Clinical Sciences (SICS), Agency for Science and Technology Research (A*STAR), 30 Medical Drive, 117609 Singapore.,8 Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 1E Kent Ridge Road, 119228 Singapore
| | - K M Godfrey
- 12 MRC Lifecourse Epidemiology Unit, University of Southampton and University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton SO16 6YD, United Kingdom.,13 NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, MP 218 Tremona Road, SO16 6YD Southampton, United Kingdom
| | - J D Holbrook
- 2 Singapore Institute for Clinical Sciences (SICS), Agency for Science and Technology Research (A*STAR), 30 Medical Drive, 117609 Singapore.,13 NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, MP 218 Tremona Road, SO16 6YD Southampton, United Kingdom
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58
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Salter SJ, Turner C, Watthanaworawit W, de Goffau MC, Wagner J, Parkhill J, Bentley SD, Goldblatt D, Nosten F, Turner P. A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children. PLoS Negl Trop Dis 2017; 11:e0005975. [PMID: 28968382 PMCID: PMC5638608 DOI: 10.1371/journal.pntd.0005975] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 10/12/2017] [Accepted: 09/19/2017] [Indexed: 11/19/2022] Open
Abstract
A longitudinal study was undertaken in infants living in the Maela refugee camp on the Thailand-Myanmar border between 2007 and 2010. Nasopharyngeal swabs were collected monthly, from birth to 24 months of age, with additional swabs taken if the infant was diagnosed with pneumonia according to WHO clinical criteria. At the time of collection, swabs were cultured for Streptococcus pneumoniae and multiple serotype carriage was assessed. The bacterial 16S rRNA gene profiles of 544 swabs from 21 infants were analysed to see how the microbiota changes with age, respiratory infection, antibiotic consumption and pneumococcal acquisition. The nasopharyngeal microbiota is a somewhat homogenous community compared to that of other body sites. In this cohort it is dominated by five taxa: Moraxella, Streptococcus, Haemophilus, Corynebacterium and an uncharacterized Flavobacteriaceae taxon of 93% nucleotide similarity to Ornithobacterium. Infant age correlates with certain changes in the microbiota across the cohort: Staphylococcus and Corynebacterium are associated with the first few months of life while Moraxella and the uncharacterised Flavobacteriaceae increase in proportional abundance with age. Respiratory illness and antibiotic use often coincide with an unpredictable perturbation of the microbiota that differs from infant to infant and in different illness episodes. The previously described interaction between Dolosigranulum and Streptococcus was observed in these data. Monthly sampling demonstrates that the nasopharyngeal microbiota is in flux throughout the first two years of life, and that in this refugee camp population the pool of potential bacterial colonisers may be limited. The nasopharynx hosts a community of microbes that first colonise us during infancy and that changes as we grow. Colonisation with certain species is a risk factor for developing respiratory infections such as pneumonia, while other species can have a protective influence. In this study we use molecular methods to identify the bacteria present in nasopharyngeal swabs taken regularly from children in a refugee camp in Thailand. The microbiota develops with age, with early colonisers such as Corynebacterium or Staphylococcus being eventually outgrown by Moraxella and an uncultured taxon described here as unclassified Flavobacteriaceae I. There is evidence in the cohort of Streptococcus pneumoniae being frequently carried and transmitted throughout the first two years of life. We found that the microbiota profiles were not unique or distinguishable between individuals in this study, which is unlike studies in high income, low density populations.
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Affiliation(s)
- Susannah J. Salter
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail:
| | - Claudia Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | - Josef Wagner
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - David Goldblatt
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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59
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Kelly MS, Surette MG, Smieja M, Pernica JM, Rossi L, Luinstra K, Steenhoff AP, Feemster KA, Goldfarb DM, Arscott-Mills T, Boiditswe S, Rulaganyang I, Muthoga C, Gaofiwe L, Mazhani T, Rawls JF, Cunningham CK, Shah SS, Seed PC. The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana. Pediatr Infect Dis J 2017; 36:e211-e218. [PMID: 28399056 PMCID: PMC5555803 DOI: 10.1097/inf.0000000000001607] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Nearly half of child pneumonia deaths occur in sub-Saharan Africa. Microbial communities in the nasopharynx are a reservoir for pneumonia pathogens and remain poorly described in African children. METHODS Nasopharyngeal swabs were collected from children with pneumonia (N = 204), children with upper respiratory infection symptoms (N = 55) and healthy children (N = 60) in Botswana between April 2012 and April 2014. We sequenced the V3 region of the bacterial 16S ribosomal RNA gene and used partitioning around medoids to cluster samples into microbiota biotypes. We then used multivariable logistic regression to examine whether microbiota biotypes were associated with pneumonia and upper respiratory infection symptoms. RESULTS Mean ages of children with pneumonia, children with upper respiratory infection symptoms and healthy children were 8.2, 11.4 and 8.0 months, respectively. Clustering of nasopharyngeal microbiota identified 5 distinct biotypes: Corynebacterium/Dolosigranulum-dominant (23%), Haemophilus-dominant (11%), Moraxella-dominant (24%), Staphylococcus-dominant (13%) and Streptococcus-dominant (28%). The Haemophilus-dominant [odds ratio (OR): 13.55; 95% confidence interval (CI): 2.10-87.26], the Staphylococcus-dominant (OR: 8.27; 95% CI: 2.13-32.14) and the Streptococcus-dominant (OR: 39.97; 95% CI: 6.63-241.00) biotypes were associated with pneumonia. The Moraxella-dominant (OR: 3.71; 95% CI: 1.09-12.64) and Streptococcus-dominant (OR: 12.26; 95% CI: 1.81-83.06) biotypes were associated with upper respiratory infection symptoms. In children with pneumonia, HIV infection was associated with a lower relative abundance of Dolosigranulum (P = 0.03). CONCLUSIONS Pneumonia and upper respiratory infection symptoms are associated with distinct nasopharyngeal microbiota biotypes in African children. A lower abundance of the commensal genus Dolosigranulum may contribute to the higher pneumonia risk of HIV-infected children.
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Affiliation(s)
- Matthew S. Kelly
- Botswana-UPenn Partnership, Gaborone, Botswana
- Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | | | - Marek Smieja
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- St. Joseph’s Healthcare, Hamilton, Ontario, Canada
| | - Jeffrey M. Pernica
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Laura Rossi
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Andrew P. Steenhoff
- Botswana-UPenn Partnership, Gaborone, Botswana
- Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristen A. Feemster
- Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - David M. Goldfarb
- Botswana-UPenn Partnership, Gaborone, Botswana
- Department of Pathology and Laboratory Medicine, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Tonya Arscott-Mills
- Botswana-UPenn Partnership, Gaborone, Botswana
- Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | | | | | - Tiny Mazhani
- University of Botswana School of Medicine, Gaborone, Botswana
| | - John F. Rawls
- Center for the Genomics of Microbial Systems, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC
| | - Coleen K. Cunningham
- Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Samir S. Shah
- Divisions of Hospital Medicine and Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Patrick C. Seed
- Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, NC, USA
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60
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Rescigno M. The microbiota revolution: Excitement and caution. Eur J Immunol 2017; 47:1406-1413. [PMID: 28675439 DOI: 10.1002/eji.201646576] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/05/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022]
Abstract
Scientific progress is characterized by important technological advances. Next-generation DNA sequencing has, in the past few years, led to a major scientific revolution: the microbiome revolution. It has become possible to generate a fingerprint of the whole microbiota of any given environment. As it becomes clear that the microbiota affects several aspects of our lives, each new scientific finding should ideally be analyzed in light of these communities. For instance, animal experimentation should consider animal sources and husbandry; human experimentation should include analysis of microenvironmental cues that might affect the microbiota, including diet, antibiotic, and drug use, genetics. When analyzing the activity of a drug, we should remember that, according to the microbiota of the host, different drug activities might be observed, either due to modification or degradation by the microbiota, or because the microbiota changes the immune system of the host in a way that makes that drug more or less effective. This minireview will not be a comprehensive review on the interaction between the host and microbiota, but it will aim at creating awareness on why we should not forget the contribution of the microbiota in any single aspect of biology.
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Affiliation(s)
- Maria Rescigno
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.,Dipartimento di Scienze della Salute, Universita' di Milano, Milan, Italy
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61
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Mika M, Maurer J, Korten I, Allemann A, Aebi S, Brugger SD, Qi W, Frey U, Latzin P, Hilty M. Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case-control study. MICROBIOME 2017; 5:85. [PMID: 28738889 PMCID: PMC5525364 DOI: 10.1186/s40168-017-0302-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/06/2017] [Indexed: 05/31/2023]
Abstract
BACKGROUND Bacterial colonization of the upper airways is a prerequisite for subsequent invasive disease. With the introduction of the 7- and 13-valent pneumococcal conjugate vaccines (PCV7 and PCV13), changes in pneumococcal upper airway colonization have been described. It is, however, less evident whether the vaccines lead to compositional changes of the upper airway microbiota. Here, we performed a case-control study using samples from a longitudinal infant cohort from Switzerland. We compared pneumococcal carriage and the nasal microbiota within the first year of life of healthy infants vaccinated with either PCV7 (n = 20, born in 2010) or PCV13 (n = 21, born between 2011 and 2013). Nasal swabs were collected every second week (n = 763 in total). Pneumococcal carriage was analyzed by quantitative PCR of the pneumococcal-specific lytA gene. Analysis of the bacterial core microbiota was performed based on 16S rRNA sequencing and subsequent oligotyping. We exclusively performed oligotyping of the core microbiota members, which were defined as the five most abundant bacterial families (Moraxellaceae, Streptococcaceae, Staphylococcaceae, Corynebacteriaceae, and Pasteurellaceae). Linear mixed effect (LME) and negative binomial regression models were used for statistical analyses. RESULTS We found a higher number of samples positive for pneumococcal carriage in PCV7- compared to PCV13-vaccinated infants (LME model; P = 0.01). In contrast, infants vaccinated in the PCV13 era had an increased alpha diversity as measured by the richness and the Shannon Diversity Index (LME model; P = 0.003 and P = 0.01, respectively). Accordingly, the PCV13 era was associated with clusters of a higher diversity than PCV7-associated clusters. Furthermore, infants vaccinated with PCV13 had a higher binary-based within-subject microbiota similarity, as well as a decreased Jensen-Shannon distance over time as compared to PCV7-vaccinated infants, indicating a higher microbiota stability in the PCV13 era (LME model and t test; P = 0.06 and P = 0.03, respectively). CONCLUSIONS We hypothesize that the higher diversity and stability of the upper airway microbiota in the PCV13 era is the result of the lower pneumococcal carriage rate. This seems to indicate that the nasal bacterial microbiota of infants has changed in recent years as compared to the beginning of this study.
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Affiliation(s)
- Moana Mika
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Josua Maurer
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
| | - Insa Korten
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Aurélie Allemann
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
| | - Silvio D Brugger
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Weihong Qi
- Functional Genomics Center, Swiss Federal Institute of Technology Zurich/University of Zurich, Zurich, Switzerland
| | - Urs Frey
- University Children's Hospital (UKBB), Basel, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland.
- Department of Infectious Diseases, University Hospital, Bern, Switzerland.
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62
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Chonmaitree T, Jennings K, Golovko G, Khanipov K, Pimenova M, Patel JA, McCormick DP, Loeffelholz MJ, Fofanov Y. Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media. PLoS One 2017; 12:e0180630. [PMID: 28708872 PMCID: PMC5510840 DOI: 10.1371/journal.pone.0180630] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/18/2017] [Indexed: 01/21/2023] Open
Abstract
Background Interferences between pathogenic bacteria and specific commensals are known. We determined the interactions between nasopharyngeal microbial pathogens and commensals during viral upper respiratory tract infection (URI) and acute otitis media (AOM) in infants. Methods We analyzed 971 specimens collected monthly and during URI and AOM episodes from 139 infants. The 16S rRNA V4 gene regions were sequenced on the Illumina MiSeq platform. Results Among the high abundant genus-level nasopharyngeal microbiota were Moraxella, Haemophilus, and Streptococcus (3 otopathogen genera), Corynebacterium, Dolosigranulum, Staphylococcus, Acinetobacter, Pseudomonas, and Bifidobacterium. Bacterial diversity was lower in culture-positive samples for Streptococcus pneumoniae, and Haemophilus influenzae, compared to cultured-negative samples. URI frequencies were positively associated with increasing trend in otopathogen colonization. AOM frequencies were associated with decreasing trend in Micrococcus colonization. During URI and AOM, there were increases in abundance of otopathogen genera and decreases in Pseudomonas, Myroides, Yersinia, and Sphingomonas. Otopathogen abundance was increased during symptomatic viral infection, but not during asymptomatic infection. The risk for AOM complicating URI was reduced by increased abundance of Staphylococcus and Sphingobium. Conclusion Otopathogen genera played the key roles in URI and AOM occurrences. Staphylococcus counteracts otopathogens thus Staphylococcal colonization may be beneficial, rather than harmful. While Sphingobium may play a role in preventing AOM complicating URI, the commonly used probiotic Bifidobacterium did not play a significant role during URI or AOM. The role of less common commensals in counteracting the deleterious effects of otopathogens requires further studies.
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Affiliation(s)
- Tasnee Chonmaitree
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States of America
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
- * E-mail:
| | - Kristofer Jennings
- Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Georgiy Golovko
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Kamil Khanipov
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Maria Pimenova
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Janak A. Patel
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States of America
| | - David P. McCormick
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Michael J. Loeffelholz
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Yuriy Fofanov
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
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63
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Köhling HL, Plummer SF, Marchesi JR, Davidge KS, Ludgate M. The microbiota and autoimmunity: Their role in thyroid autoimmune diseases. Clin Immunol 2017; 183:63-74. [PMID: 28689782 DOI: 10.1016/j.clim.2017.07.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 07/02/2017] [Accepted: 07/05/2017] [Indexed: 12/11/2022]
Abstract
Since the 1970s, the role of infectious diseases in the pathogenesis of Graves' disease (GD) has been an object of intensive research. The last decade has witnessed many studies on Yersinia enterocolitica, Helicobacter pylori and other bacterial organisms and their potential impact on GD. Retrospective, prospective and molecular binding studies have been performed with contrary outcomes. Until now it is not clear whether bacterial infections can trigger autoimmune thyroid disease. Common risk factors for GD (gender, smoking, stress, and pregnancy) reveal profound changes in the bacterial communities of the gut compared to that of healthy controls but a pathogenetic link between GD and dysbiosis has not yet been fully elucidated. Conventional bacterial culture, in vitro models, next generation and high-throughput DNA sequencing are applicable methods to assess the impact of bacteria in disease onset and development. Further studies on the involvement of bacteria in GD are needed and may contribute to the understanding of pathogenetic processes. This review will examine available evidence on the subject.
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Affiliation(s)
- Hedda L Köhling
- University Hopital Essen, Institute of Medical Microbiology, Essen, Germany; Cultech Ltd., Baglan, Port Talbot, United Kingdom.
| | | | - Julian R Marchesi
- School of Biosciences, Cardiff University, Cardiff, United Kingdom; Centre for Digestive and Gut Health, Imperial College London, London, W2 1NY, United Kingdom
| | | | - Marian Ludgate
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
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64
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Dorn ES, Tress B, Suchodolski JS, Nisar T, Ravindran P, Weber K, Hartmann K, Schulz BS. Bacterial microbiome in the nose of healthy cats and in cats with nasal disease. PLoS One 2017; 12:e0180299. [PMID: 28662139 PMCID: PMC5491177 DOI: 10.1371/journal.pone.0180299] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 06/13/2017] [Indexed: 12/22/2022] Open
Abstract
Background Traditionally, changes in the microbial population of the nose have been assessed using conventional culture techniques. Sequencing of bacterial 16S rRNA genes demonstrated that the human nose is inhabited by a rich and diverse bacterial microbiome that cannot be detected using culture-based methods. The goal of this study was to describe the nasal microbiome of healthy cats, cats with nasal neoplasia, and cats with feline upper respiratory tract disease (FURTD). Methodology/Principal findings DNA was extracted from nasal swabs of healthy cats (n = 28), cats with nasal neoplasia (n = 16), and cats with FURTD (n = 15), and 16S rRNA genes were sequenced. High species richness was observed in all samples. Rarefaction analysis revealed that healthy cats living indoors had greater species richness (observed species p = 0.042) and Shannon diversity (p = 0.003) compared with healthy cats living outdoors. Higher species richness (observed species p = 0.001) and Shannon diversity (p<0.001) were found in middle-aged cats in comparison to healthy cats in different age groups. Principal coordinate analysis revealed separate clustering based on similarities in bacterial molecular phylogenetic trees of 16S rRNA genes for indoor and outdoor cats. In all groups examined, the most abundant phyla identified were Proteobacteria, Firmicutes, and Bacteroidetes. At the genus level, 375 operational taxonomic units (OTUs) were identified. In healthy cats and cats with FURTD, Moraxella spp. was the most common genus, while it was unclassified Bradyrhizobiaceae in cats with nasal neoplasia. High individual variability was observed. Conclusion This study demonstrates that the nose of cats is inhabited by much more variable and diverse microbial communities than previously shown. Future research in this field might help to develop new diagnostic tools to easily identify nasal microbial changes, relate them to certain disease processes, and help clinicians in the decision process of antibiotic selection for individual patients.
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Affiliation(s)
- Elisabeth S. Dorn
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Barbara Tress
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Tariq Nisar
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Prajesh Ravindran
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Karin Weber
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Katrin Hartmann
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Bianka S. Schulz
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
- * E-mail:
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65
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Liu AH, Anderson WC, Dutmer CM, Searing DA, Szefler SJ. Advances in asthma 2015: Across the lifespan. J Allergy Clin Immunol 2017; 138:397-404. [PMID: 27497278 DOI: 10.1016/j.jaci.2016.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 12/19/2022]
Abstract
In 2015, progress in understanding asthma ranged from insights to asthma inception, exacerbations, and severity to advancements that will improve disease management throughout the lifespan. 2015's insights to asthma inception included how the intestinal microbiome affects asthma expression with the identification of specific gastrointestinal bacterial taxa in early infancy associated with less asthma risk, possibly by promoting regulatory immune development at a critical early age. The relevance of epigenetic mechanisms in regulating asthma-related gene expression was strengthened. Predicting and preventing exacerbations throughout life might help to reduce progressive lung function decrease and disease severity in adulthood. Although allergy has long been linked to asthma exacerbations, a mechanism through which IgE impairs rhinovirus immunity and underlies asthma exacerbations was demonstrated and improved by anti-IgE therapy (omalizumab). Other key molecular pathways underlying asthma exacerbations, such as cadherin-related family member 3 (CDHR3) and orosomucoid like 3 (ORMDL3), were elucidated. New anti-IL-5 therapeutics, mepolizumab and reslizumab, were US Food and Drug Administration approved for the treatment of patients with severe eosinophilic asthma. In a clinical trial the novel therapeutic inhaled GATA3 mRNA-specific DNAzyme attenuated early- and late-phase allergic responses to inhaled allergen. These current findings are significant steps toward addressing unmet needs in asthma prevention, severity modification, disparities, and lifespan outcomes.
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Affiliation(s)
- Andrew H Liu
- Breathing Institute and Pulmonary Medicine Section, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colo.
| | - William C Anderson
- Allergy & Immunology Section, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colo
| | - Cullen M Dutmer
- Allergy & Immunology Section, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colo
| | - Daniel A Searing
- Allergy & Immunology Section, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colo
| | - Stanley J Szefler
- Breathing Institute and Pulmonary Medicine Section, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colo
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Akmatov MK, Koch N, Vital M, Ahrens W, Flesch-Janys D, Fricke J, Gatzemeier A, Greiser H, Günther K, Illig T, Kaaks R, Krone B, Kühn A, Linseisen J, Meisinger C, Michels K, Moebus S, Nieters A, Obi N, Schultze A, Six-Merker J, Pieper DH, Pessler F. Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study - findings from Pretest 1 of the German National Cohort. Sci Rep 2017; 7:1855. [PMID: 28500287 PMCID: PMC5431815 DOI: 10.1038/s41598-017-01212-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/27/2017] [Indexed: 12/13/2022] Open
Abstract
We examined acceptability, preference and feasibility of collecting nasal and oropharyngeal swabs, followed by microbiome analysis, in a population-based study with 524 participants. Anterior nasal and oropharyngeal swabs were collected by certified personnel. In addition, participants self-collected nasal swabs at home four weeks later. Four swab types were compared regarding (1) participants' satisfaction and acceptance and (2) detection of microbial community structures based on deep sequencing of the 16 S rRNA gene V1-V2 variable regions. All swabbing methods were highly accepted. Microbial community structure analysis revealed 846 phylotypes, 46 of which were unique to oropharynx and 164 unique to nares. The calcium alginate tipped swab was found unsuitable for microbiome determinations. Among the remaining three swab types, there were no differences in oropharyngeal microbiomes detected and only marginal differences in nasal microbiomes. Microbial community structures did not differ between staff-collected and self-collected nasal swabs. These results suggest (1) that nasal and oropharyngeal swabbing are highly feasible methods for human population-based studies that include the characterization of microbial community structures in these important ecological niches, and (2) that self-collection of nasal swabs at home can be used to reduce cost and resources needed, particularly when serial measurements are to be taken.
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Affiliation(s)
- Manas K Akmatov
- TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany. .,Helmholtz Centre for Infection Research, Braunschweig, Germany. .,Centre for Individualised Infection Medicine, Hannover, Germany.
| | - Nadine Koch
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marius Vital
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Wolfgang Ahrens
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Bremen, Germany
| | - Dieter Flesch-Janys
- University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Fricke
- Division of Cancer Epidemiology, German Cancer Research Centre, Heidelberg, Germany.,Institute for Social Medicine, Epidemiology and Health Economics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anja Gatzemeier
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Halina Greiser
- Division of Cancer Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Kathrin Günther
- Leibniz Institute for Prevention Research and Epidemiology-BIPS, Bremen, Germany
| | - Thomas Illig
- Institute of Molecular Epidemiology, Helmholtz Centre Munich, Munich, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Centre, Heidelberg, Germany
| | - Bastian Krone
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Andrea Kühn
- Institute of Molecular Epidemiology, Helmholtz Centre Munich, Munich, Germany
| | - Jakob Linseisen
- Institute of Epidemiology 2, Helmholtz Centre Munich, Munich, Germany
| | - Christine Meisinger
- Institute of Epidemiology 2, Helmholtz Centre Munich, Munich, Germany.,Klinikum Augsburg, KORA and NAKO Study Center, Augsburg, Germany
| | - Karin Michels
- Institute for Prevention and Cancer Epidemiology, University Medical Center Freiburg, Freiburg, Germany
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, Essen, Germany
| | - Alexandra Nieters
- Centre for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Nadia Obi
- University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anja Schultze
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Julia Six-Merker
- Institute of Epidemiology 2, Helmholtz Centre Munich, Munich, Germany.,Institute for Prevention and Cancer Epidemiology, University Medical Center Freiburg, Freiburg, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Frank Pessler
- TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany.,Centre for Individualised Infection Medicine, Hannover, Germany
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67
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Chiu CY, Chan YL, Tsai YS, Chen SA, Wang CJ, Chen KF, Chung IF. Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood. Sci Rep 2017; 7:1820. [PMID: 28500319 PMCID: PMC5431806 DOI: 10.1038/s41598-017-02067-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/10/2017] [Indexed: 12/15/2022] Open
Abstract
Microbiota plays an important role in regulating immune responses associated with atopic diseases. We sought to evaluate relationships among airway microbiota, serum IgE levels, allergic sensitization and their relevance to rhinitis and asthma. Microbial characterization was performed using Illumina-based 16S rRNA gene sequencing of 87 throat swabs collected from children with asthma (n = 32) and rhinitis (n = 23), and from healthy controls (n = 32). Data analysis was performed using QIIME (Quantitative Insights Into Microbial Ecology) v1.8. Significantly higher abundance of Proteobacteria was found in children with rhinitis than in the healthy controls (20.1% vs. 16.1%, P = 0.009). Bacterial species richness (Chao1 index) and diversity (Shannon index) were significantly reduced in children with mite sensitization but not in those with food or IgE sensitization. Compared with healthy children without mite sensitization, the mite-sensitized children with rhinitis and asthma showed significantly lower Chao1 and Shannon indices. Moraxella and Leptotrichia species were significantly found in the interaction of mite sensitization with rhinitis and asthma respectively. Airway microbial diversity appears to be inversely associated with sensitization to house dust mites. A modulation between airway dysbiosis and responses to allergens may potentially cause susceptibility to rhinitis and asthma in early childhood.
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Affiliation(s)
- Chih-Yung Chiu
- Department of Pediatrics, Chang Gung Memorial Hospital at Keelung, and Chang Gung University, Taoyuan, Taiwan. .,Division of Pediatric Pulmonology, Department of Pediatrics, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan, Taiwan.
| | - Yi-Ling Chan
- Department of Emergency Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Yu-Shuen Tsai
- The Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ssu-An Chen
- The Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Jung Wang
- Department of Pediatrics, Chang Gung Memorial Hospital at Keelung, and Chang Gung University, Taoyuan, Taiwan
| | - Kuan-Fu Chen
- Department of Emergency Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - I-Fang Chung
- The Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan. .,The Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, Taiwan.
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68
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Man WH, de Steenhuijsen Piters WA, Bogaert D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol 2017; 15:259-270. [PMID: 28316330 PMCID: PMC7097736 DOI: 10.1038/nrmicro.2017.14] [Citation(s) in RCA: 707] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The respiratory tract is a complex organ system that is responsible for the exchange of oxygen and carbon dioxide. The human respiratory tract spans from the nostrils to the lung alveoli and is inhabited by niche-specific communities of bacteria. The microbiota of the respiratory tract probably acts as a gatekeeper that provides resistance to colonization by respiratory pathogens. The respiratory microbiota might also be involved in the maturation and maintenance of homeostasis of respiratory physiology and immunity. The ecological and environmental factors that direct the development of microbial communities in the respiratory tract and how these communities affect respiratory health are the focus of current research. Concurrently, the functions of the microbiome of the upper and lower respiratory tract in the physiology of the human host are being studied in detail. In this Review, we will discuss the epidemiological, biological and functional evidence that support the physiological role of the respiratory microbiota in the maintenance of human health.
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Affiliation(s)
- Wing Ho Man
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA The Netherlands
- Spaarne Gasthuis Academy, Spaarnepoort 1, Hoofddorp, 2134 TM The Netherlands
| | - Wouter A.A. de Steenhuijsen Piters
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA The Netherlands
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ UK
| | - Debby Bogaert
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA The Netherlands
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ UK
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Abstract
Landscape ecology examines the relationships between the spatial arrangement of different landforms and the processes that give rise to spatial and temporal patterns in local community structure. The spatial ecology of the microbial communities that inhabit the human body-in particular, those of the nose, mouth, and throat-deserves greater attention. Important questions include what defines the size of a population (i.e., "patch") in a given body site, what defines the boundaries of distinct patches within a single body site, and where and over what spatial scales within a body site are gradients detected. This Review looks at the landscape ecology of the upper respiratory tract and mouth and seeks greater clarity about the physiological factors-whether immunological, chemical, or physical-that govern microbial community composition and function and the ecological traits that underlie health and disease.
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Affiliation(s)
- Diana M Proctor
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A Relman
- Department of Microbiology & 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.
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70
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Perez GF, Pérez-Losada M, Isaza N, Rose MC, Colberg-Poley AM, Nino G. Nasopharyngeal microbiome in premature infants and stability during rhinovirus infection. J Investig Med 2017; 65:984-990. [PMID: 28363939 DOI: 10.1136/jim-2017-000414] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2017] [Indexed: 12/21/2022]
Abstract
RATIONALE The nasopharyngeal (NP) microbiota of newborns and infants plays a key role in modulating airway inflammation and respiratory symptoms during viral infections. Premature (PM) birth modifies the early NP environment and is a major risk factor for severe viral respiratory infections. However, it is currently unknown if the NP microbiota of PM infants is altered relative to full-term (FT) individuals. OBJECTIVES To characterize the NP microbiota differences in preterm and FT infants during rhinovirus (RV) infection. METHODS We determined the NP microbiota of infants 6 months to ≤2 years of age born FT (n=6) or severely PM<32 weeks gestation (n=7). We compared microbiota composition in healthy NP samples and performed a longitudinal analysis during naturally occurring RV infections to contrast the microbiota dynamics in PM versus FT infants. RESULTS We observed significant differences in the NP bacterial community of PM versus FT. NP from PM infants had higher within-group dissimilarity (heterogeneity) relative to FT infants. Bacterial composition of NP samples from PM infants showed increased Proteobacteria and decreased in Firmicutes. There were also differences in the major taxonomic groups identified, including Streptococcus, Moraxella, and Haemophilus. Longitudinal data showed that these prematurity-related microbiota features persisted during RV infection. CONCLUSIONS PM is associated with NP microbiota changes beyond the neonatal stage. PM infants have an NP microbiota with high heterogeneity relative to FT infants. These prematurity-related microbiota features persisted during RV infection, suggesting that the NP microbiota of PM may play an important role in modulating airway inflammatory and immune responses in this vulnerable group.
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Affiliation(s)
- Geovanny F Perez
- Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Department of Integrative Systems Biology, George Washington University, Washington, DC, USA.,Center for Genetic Medicine Research, Children's National Health System, Washington, DC, USA
| | - Marcos Pérez-Losada
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC, USA.,Computational Biology Institute, George Washington University, Ashburn, Virginia, USA.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Natalia Isaza
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Division of Neonatology, Children's National Medical Center, Washington, DC, USA
| | - Mary C Rose
- Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Department of Integrative Systems Biology, George Washington University, Washington, DC, USA.,Center for Genetic Medicine Research, Children's National Health System, Washington, DC, USA.,Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC, USA
| | - Anamaris M Colberg-Poley
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Department of Integrative Systems Biology, George Washington University, Washington, DC, USA.,Center for Genetic Medicine Research, Children's National Health System, Washington, DC, USA.,Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC, USA
| | - Gustavo Nino
- Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, USA.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Department of Integrative Systems Biology, George Washington University, Washington, DC, USA.,Center for Genetic Medicine Research, Children's National Health System, Washington, DC, USA
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71
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Mortensen MS, Brejnrod AD, Roggenbuck M, Abu Al-Soud W, Balle C, Krogfelt KA, Stokholm J, Thorsen J, Waage J, Rasmussen MA, Bisgaard H, Sørensen SJ. The developing hypopharyngeal microbiota in early life. MICROBIOME 2016; 4:70. [PMID: 28038686 PMCID: PMC5203717 DOI: 10.1186/s40168-016-0215-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/01/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND The airways of healthy humans harbor a distinct microbial community. Perturbations in the microbial community have been associated with disease, yet little is known about the formation and development of a healthy airway microbiota in early life. Our goal was to understand the establishment of the airway microbiota within the first 3 months of life. We investigated the hypopharyngeal microbiota in the unselected COPSAC2010 cohort of 700 infants, using 16S rRNA gene sequencing of hypopharyngeal aspirates from 1 week, 1 month, and 3 months of age. RESULTS Our analysis shows that majority of the hypopharyngeal microbiota of healthy infants belong to each individual's core microbiota and we demonstrate five distinct community pneumotypes. Four of these pneumotypes are dominated by the genera Staphylococcus, Streptococcus, Moraxella, and Corynebacterium, respectively. Furthermore, we show temporal pneumotype changes suggesting a rapid development towards maturation of the hypopharyngeal microbiota and a significant effect from older siblings. Despite an overall common trajectory towards maturation, individual infants' microbiota are more similar to their own, than to others, over time. CONCLUSIONS Our findings demonstrate a consolidation of the population of indigenous bacteria in healthy airways and indicate distinct trajectories in the early development of the hypopharyngeal microbiota.
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Affiliation(s)
- Martin Steen Mortensen
- Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark
| | - Asker Daniel Brejnrod
- Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark
| | - Michael Roggenbuck
- Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark
| | - Waleed Abu Al-Soud
- Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark
| | - Christina Balle
- Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark
| | - Karen Angeliki Krogfelt
- Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen S, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, 2820, Gentofte, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, 2820, Gentofte, Denmark
| | - Johannes Waage
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, 2820, Gentofte, Denmark
| | - Morten Arendt Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, 2820, Gentofte, Denmark
- Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg C, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, 2820, Gentofte, Denmark
| | - Søren Johannes Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark.
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72
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Interactions of Respiratory Viruses and the Nasal Microbiota during the First Year of Life in Healthy Infants. mSphere 2016; 1:mSphere00312-16. [PMID: 27904883 PMCID: PMC5120172 DOI: 10.1128/msphere.00312-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/29/2016] [Indexed: 11/20/2022] Open
Abstract
Respiratory viral infections are very frequent in infancy and of importance in acute and chronic disease development. Infections with human rhinovirus (HRV) are, e.g., associated with the later development of asthma. We found that only symptomatic HRV infections were associated with acute changes in the nasal microbiota, mainly characterized by a loss of microbial diversity. Infants with more frequent symptomatic HRV infections had a lower bacterial diversity at the end of the first year of life. Whether the interaction between viruses and the microbiota is one pathway contributing to asthma development will be assessed in the follow-ups of these children. Independent of that, measurements of microbial diversity might represent a potential marker for risk of later lung disease or monitoring of early life interventions. Traditional culture techniques have shown that increased bacterial colonization is associated with viral colonization; however, the influence of viral colonization on the whole microbiota composition is less clear. We thus aimed to understand the interaction of viral infections and the nasal microbiota in early life to appraise their roles in disease development. Thirty-two healthy, unselected infants were included in this prospective longitudinal cohort study within the first year of life. Biweekly nasal swabs (n = 559) were taken, and the microbiota was analyzed by 16S rRNA pyrosequencing, and 10 different viruses and 2 atypical bacteria were characterized by real-time PCR (combination of seven duplex samples). In contrast to asymptomatic human rhinovirus (HRV) colonization, symptomatic HRV infections were associated with lower alpha diversity (Shannon diversity index [SDI]), higher bacterial density (PCR concentration), and a difference in beta diversities (Jaccard and Bray-Curtis index) of the microbiota. In addition, infants with more frequent HRV infections had a lower SDI at the end of the study period. Overall, changes in the microbiota associated with symptomatic HRV infections were characterized by a loss of microbial diversity. The interaction between HRV infections and the nasal microbiota in early life might be of importance for later disease development and indicate a potential approach for future interventions. IMPORTANCE Respiratory viral infections are very frequent in infancy and of importance in acute and chronic disease development. Infections with human rhinovirus (HRV) are, e.g., associated with the later development of asthma. We found that only symptomatic HRV infections were associated with acute changes in the nasal microbiota, mainly characterized by a loss of microbial diversity. Infants with more frequent symptomatic HRV infections had a lower bacterial diversity at the end of the first year of life. Whether the interaction between viruses and the microbiota is one pathway contributing to asthma development will be assessed in the follow-ups of these children. Independent of that, measurements of microbial diversity might represent a potential marker for risk of later lung disease or monitoring of early life interventions.
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73
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de Hoog MLA, Fortanier AC, Smit HA, Uiterwaal CPM, van der Ent CK, Schilder A, Damoiseaux RMJ, Venekamp RP, Bruijning-Verhagen P. Impact of Early-Onset Acute Otitis Media on Multiple Recurrences and Associated Health Care Use. J Pediatr 2016; 177:286-291.e1. [PMID: 27499216 DOI: 10.1016/j.jpeds.2016.06.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/23/2016] [Accepted: 06/22/2016] [Indexed: 01/21/2023]
Abstract
OBJECTIVE To quantify the critical age period of first episode of acute otitis media (AOM) and its consequences for AOM recurrences and AOM health care use. STUDY DESIGN Children enrolled in the Wheezing-Illnesses-STudy-LEidsche-Rijn cohort with at least 1 episode of AOM documented in their primary care health record before 2 years of age were followed until 6 years of age. Data on episodes of AOM and associated primary care consultations, antibiotic prescriptions, and specialist referrals were retrieved. Regression models assessed the presence and shape of the associations between age of first AOM and subsequent episodes of AOM and health care use. RESULTS A total of 796 of 2026 children (39%) experienced a first AOM before 2 years of age. Each month decrease in age at first AOM in the first 2 years of life increased the risk of developing recurrent AOM (≥3 AOM episodes in 6 months or ≥ 4 in 1 year) linearly by 6% (adjusted risk ratio: 1.06; 95% CI: 1.02-1.10). For first AOM occurring before 9 months, the cumulative 6-year primary care consultation rate increased by 8% (adjusted incidence rate ratio: 1.08; 95% CI: 1.03-1.15) and the associated specialist referral increased by 16% (adjusted risk ratio: 1.16; 95% CI: 1.07-1.27) for each month decrease in age. No associations were found between age at first AOM and total AOM episodes or antibiotic prescriptions. CONCLUSIONS The association between earlier age of first AOM and recurrent AOM as well as total health care use during childhood is particularly strong before 9 months of age.
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Affiliation(s)
- Marieke L A de Hoog
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Alexandre C Fortanier
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Henriette A Smit
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - CunoS P M Uiterwaal
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anne Schilder
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Otorhinolaryngology, University Medical Center Utrecht, Utrecht, The Netherlands; evidENT, Ear Institute, University College London, London, United Kingdom
| | - RogerA M J Damoiseaux
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Roderick P Venekamp
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Otorhinolaryngology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Patricia Bruijning-Verhagen
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands; Center for Infectious Diseases Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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74
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Abstract
Biomarkers (BMKs) are biological parameters that can be measured to predict or monitor disease severity or treatment efficacy. The induction of regulatory dendritic cells (DCs) concomitantly with a downregulation of proallergic DC2s (ie, DCs supporting the differentiation of T-helper lymphocyte type 2 cells) in the blood of patients allergic to grass pollen has been correlated with the early onset of allergen immunotherapy efficacy. The combined use of omics technologies to compare biological samples from clinical responders and nonresponders is being implemented in the context of nonhypothesis-driven approaches. Such comprehensive "panoromic" strategies help identify completely novel candidate BMKs, to be subsequently validated as companion diagnostics in large-scale clinical trials.
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Affiliation(s)
- Philippe Moingeon
- Research and Development, Stallergenes SA, 6 Rue Alexis de Tocqueville, Antony Cedex 92183, France.
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75
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Affiliation(s)
- Silvio D. Brugger
- Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, United States of America
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, United States of America
| | - Lindsey Bomar
- Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, United States of America
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, United States of America
| | - Katherine P. Lemon
- Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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76
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Marsh RL, Kaestli M, Chang AB, Binks MJ, Pope CE, Hoffman LR, Smith-Vaughan HC. The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx. MICROBIOME 2016; 4:37. [PMID: 27388563 PMCID: PMC4936249 DOI: 10.1186/s40168-016-0182-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/24/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Invasive methods requiring general anaesthesia are needed to sample the lung microbiota in young children who do not expectorate. This poses substantial challenges to longitudinal study of paediatric airway microbiota. Non-invasive upper airway sampling is an alternative method for monitoring airway microbiota; however, there are limited data describing the relationship of such results with lung microbiota in young children. In this study, we compared the upper and lower airway microbiota in young children to determine whether non-invasive upper airway sampling procedures provide a reliable measure of either lung microbiota or clinically defined differences. RESULTS The microbiota in oropharyngeal (OP) swabs, nasopharyngeal (NP) swabs and bronchoalveolar lavage (BAL) from 78 children (median age 2.2 years) with and without lung disease were characterised using 16S rRNA gene sequencing. Permutational multivariate analysis of variance (PERMANOVA) detected significant differences between the microbiota in BAL and those in both OP swabs (p = 0.0001, Pseudo-F = 12.2, df = 1) and NP swabs (p = 0.0001; Pseudo-F = 21.9, df = 1) with the NP and BAL microbiota more different than the OP and BAL, as indicated by a higher Pseudo-F value. The microbiota in combined OP and NP data (upper airways) provided a more comprehensive representation of BAL microbiota, but significant differences between the upper airway and BAL microbiota remained, albeit with a considerably smaller Pseudo-F (PERMANOVA p = 0.0001; Pseudo-F = 4.9, df = 1). Despite this overall difference, paired BAL and upper airway (OP and NP) microbiota were >50 % similar among 69 % of children. Furthermore, canonical analysis of principal coordinates (CAP analysis) detected significant differences between the microbiota from clinically defined groups when analysing either BAL (eigenvalues >0.8; misclassification rate 26.5 %) or the combined OP and NP data (eigenvalues >0.8; misclassification rate 12.2 %). CONCLUSIONS Upper airway sampling provided an imperfect, but reliable, representation of the BAL microbiota for most children in this study. We recommend inclusion of both OP and NP specimens when non-invasive upper airway sampling is needed to assess airway microbiota in young children who do not expectorate. The results of the CAP analysis suggest lower and upper airway microbiota profiles may differentiate children with chronic suppurative lung disease from those with persistent bacterial bronchitis; however, further research is needed to confirm this observation.
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Affiliation(s)
- R. L. Marsh
- />Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT 0810 Australia
| | - M. Kaestli
- />Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT 0810 Australia
- />Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT Australia
| | - A. B. Chang
- />Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT 0810 Australia
- />Queensland Children’s Medical Research Institute, Queensland University of Technology, Brisbane, QLD Australia
| | - M. J. Binks
- />Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT 0810 Australia
| | - C. E. Pope
- />Department of Pediatrics, University of Washington, Seattle, WA USA
- />Department of Microbiology, University of Washington, Seattle, WA USA
| | - L. R. Hoffman
- />Department of Pediatrics, University of Washington, Seattle, WA USA
- />Department of Microbiology, University of Washington, Seattle, WA USA
| | - H. C. Smith-Vaughan
- />Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT 0810 Australia
- />School of Medicine, Griffith University, Gold Coast, QLD Australia
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77
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Whelan FJ, Surette MG. Early life nasal microbiota in infants with cystic fibrosis. THE LANCET RESPIRATORY MEDICINE 2016; 4:595-596. [PMID: 27342262 DOI: 10.1016/s2213-2600(16)30153-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Fiona J Whelan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Michael G Surette
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
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78
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Mika M, Korten I, Qi W, Regamey N, Frey U, Casaulta C, Latzin P, Hilty M. The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study. THE LANCET RESPIRATORY MEDICINE 2016; 4:627-635. [PMID: 27180018 DOI: 10.1016/s2213-2600(16)30081-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/04/2016] [Accepted: 04/14/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND Respiratory tract infections and subsequent airway inflammation occur early in the life of infants with cystic fibrosis. However, detailed information about the microbial composition of the respiratory tract in infants with this disorder is scarce. We aimed to undertake longitudinal in-depth characterisation of the upper respiratory tract microbiota in infants with cystic fibrosis during the first year of life. METHODS We did this prospective cohort study at seven cystic fibrosis centres in Switzerland. Between Feb 1, 2011, and May 31, 2014, we enrolled 30 infants with a diagnosis of cystic fibrosis. Microbiota characterisation was done with 16S rRNA gene pyrosequencing and oligotyping of nasal swabs collected every 2 weeks from the infants with cystic fibrosis. We compared these data with data for an age-matched cohort of 47 healthy infants. We additionally investigated the effect of antibiotic treatment on the microbiota of infants with cystic fibrosis. Statistical methods included regression analyses with a multivariable multilevel linear model with random effects to correct for clustering on the individual level. FINDINGS We analysed 461 nasal swabs taken from the infants with cystic fibrosis; the cohort of healthy infants comprised 872 samples. The microbiota of infants with cystic fibrosis differed compositionally from that of healthy infants (p=0·001). This difference was also found in exclusively antibiotic-naive samples (p=0·001). The disordering was mainly, but not solely, due to an overall increase in the mean relative abundance of Staphylococcaceae in infants with cystic fibrosis compared with healthy infants (multivariable linear regression model stratified by age and adjusted for season; second month: coefficient 16·2 [95% CI 0·6-31·9]; p=0·04; third month: 17·9 [3·3-32·5]; p=0·02; fourth month: 21·1 [7·8-34·3]; p=0·002). Oligotyping analysis enabled differentiation between Staphylococcus aureus and coagulase-negative Staphylococci. Whereas the analysis showed a decrease in S aureus at and after antibiotic treatment, coagulase-negative Staphylococci increased. INTERPRETATION Our study describes compositional differences in the microbiota of infants with cystic fibrosis compared with healthy controls, and disordering of the microbiota on antibiotic administration. Besides S aureus, coagulase-negative Staphylococci also contributed to the disordering identified in these infants. These findings are clinically important in view of the crucial role that bacterial pathogens have in the disease progression of cystic fibrosis in early life. Our findings could be used to inform future studies of the effect of antibiotic treatment on the microbiota in infants with cystic fibrosis, and could assist in the prevention of early disease progression in infants with this disorder. FUNDING Swiss National Science Foundation, Fondation Botnar, the Swiss Society for Cystic Fibrosis, and the Swiss Lung Association Bern.
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Affiliation(s)
- Moana Mika
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Insa Korten
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland; Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland; University Children's Hospital (UKBB), Basel, Switzerland
| | - Weihong Qi
- Functional Genomics Center, Swiss Federal Institute of Technology Zurich, University of Zurich, Zurich, Switzerland
| | - Nicolas Regamey
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland; Children's Hospital, Lucerne, Switzerland
| | - Urs Frey
- University Children's Hospital (UKBB), Basel, Switzerland
| | - Carmen Casaulta
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland; University Children's Hospital (UKBB), Basel, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland.
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79
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Abstract
The respiratory tract, once believed to be sterile, harbors diverse bacterial communities. The role of microorganisms within health and disease is slowly being unraveled. Evidence points to the neonatal period as a critical time for establishing stable bacterial communities and influencing immune responses important for long-term respiratory health. This review summarizes the evidence of early airway and lung bacterial colonization and the role the microbiome has on respiratory health in the short and long term. The challenges of neonatal respiratory microbiome studies and future research directions are also discussed.
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Affiliation(s)
- David J Gallacher
- Department of Child Health, School of Medicine, Cardiff University , Cardiff , UK
| | - Sailesh Kotecha
- Department of Child Health, School of Medicine, Cardiff University , Cardiff , UK
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