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This study of healthy adults revealed no major changes in the bacterial community of the respiratory tracts following RSV inoculation, suggesting that the adult respiratory microbial community is resilient to viral perturbations https://bit.ly/3AwnMc8

Introduction: The airway microbiota has been linked to specific paediatric respiratory diseases, but studies are often small. It remains unclear whether particular bacteria are associated with a given disease, or if a more general, non-specific microbiota association with disease exists, as suggested for the gut. We investigated overarching patterns of bacterial association with acute and chronic paediatric respiratory disease in an individual participant data (IPD) meta-analysis of 16S rRNA gene sequences from published respiratory microbiota studies. Methods: We obtained raw microbiota data from public repositories or via communication with corresponding authors. Cross-sectional analyses of the paediatric (<18 years) microbiota in acute and chronic respiratory conditions, with >10 case subjects were included. Sequence data were processed using a uniform bioinformatics pipeline, removing a potentially substantial source of variation. Microbiota differences across diagnoses were assessed using alpha- and beta-diversity approaches, machine learning, and biomarker analyses. Results: We ultimately included 20 studies containing individual data from 2624 children. Disease was associated with lower bacterial diversity in nasal and lower airway samples and higher relative abundances of specific nasal taxa including Streptococcus and Haemophilus. Machine learning success in assigning samples to diagnostic groupings varied with anatomical site, with positive predictive value and sensitivity ranging from 43 to 100 and 8 to 99%, respectively. Conclusion: IPD meta-analysis of the respiratory microbiota across multiple diseases allowed identification of a non-specific disease association which cannot be recognised by studying a single disease. Whilst imperfect, machine learning offers promise as a potential additional tool to aid clinical diagnosis.

© 2020 The Author(s). Background: Chronic infection and concomitant airway inflammation is the leading cause of morbidity and mortality for people living with cystic fibrosis (CF). Although chronic infection in CF is undeniably polymicrobial, involving a lung microbiota, infection surveillance and control approaches remain underpinned by classical aerobic culture-based microbiology. How to use microbiomics to direct clinical management of CF airway infections remains a crucial challenge. A pivotal step towards leveraging microbiome approaches in CF clinical care is to understand the ecology of the CF lung microbiome and identify ecological patterns of CF microbiota across a wide spectrum of lung disease. Assessing sputum samples from 299 patients attending 13 CF centres in Europe and the USA, we determined whether the emerging relationship of decreasing microbiota diversity with worsening lung function could be considered a generalised pattern of CF lung microbiota and explored its potential as an informative indicator of lung disease state in CF. Results: We tested and found decreasing microbiota diversity with a reduction in lung function to be a significant ecological pattern. Moreover, the loss of diversity was accompanied by an increase in microbiota dominance. Subsequently, we stratified patients into lung disease categories of increasing disease severity to further investigate relationships between microbiota characteristics and lung function, and the factors contributing to microbiota variance. Core taxa group composition became highly conserved within the severe disease category, while the rarer satellite taxa underpinned the high variability observed in the microbiota diversity. Further, the lung microbiota of individual patient were increasingly dominated by recognised CF pathogens as lung function decreased. Conversely, other bacteria, especially obligate anaerobes, increasingly dominated in those with better lung function. Ordination analyses revealed l

© 2016, BMJ Publishing Group. All rights reserved. Objective: To determine the existence of mucosal dysbiosis in siblings of patients with Crohn's disease (CD) using 454 pyrosequencing and to comprehensively characterise and determine the influence of genotypical and phenotypical factors, on that dysbiosis. Siblings of patients with CD have elevated risk of developing CD and display aspects of disease phenotype, including faecal dysbiosis. Whether the mucosal microbiota is disrupted in these at-risk individuals is unknown. Design: Rectal biopsy DNA was extracted from 21 patients with quiescent CD, 17 of their healthy siblings and 19 unrelated healthy controls. Mucosal microbiota was analysed by 16S rRNA gene pyrosequencing and were classified into core and rare species. Genotypical risk was determined using Illumina Immuno BeadChip, faecal calprotectin by ELISA and blood T-cell phenotype by flow cytometry. Results: Core microbiota of both patients with CD and healthy siblings was significantly less diverse than controls. Metacommunity profiling (Bray-Curtis (SBC) index) showed the sibling core microbial composition to be more similar to CD (SBC=0.70) than to healthy controls, whereas the sibling rare microbiota was more similar to healthy controls (SBC=0.42). Faecalibacterium prausnitzii contributed most to core metacommunity dissimilarity both between siblings and controls, and between patients and controls. Phenotype/genotype markers of CD risk significantly influenced microbiota variation between and within groups, of which genotype had the largest effect. Conclusions: Individuals with elevated CD-risk display mucosal dysbiosis characterised by reduced diversity of core microbiota and lower abundance of F. prausnitzii. This dysbiosis in healthy people at risk of CD implicates microbiological processes in CD pathogenesis.

© 2016 International Society for Microbial Ecology All rights reserved. Pulmonary symptoms in cystic fibrosis (CF) begin in early life with chronic lung infections and concomitant airway inflammation leading to progressive loss of lung function. Gradual pulmonary function decline is interspersed with periods of acute worsening of respiratory symptoms known as CF pulmonary exacerbations (CFPEs). Cumulatively, CFPEs are associated with more rapid disease progression. In this study multiple sputum samples were collected from adult CF patients over the course of CFPEs to better understand how changes in microbiota are associated with CFPE onset and management. Data were divided into five clinical periods: pre-CFPE baseline, CFPE, antibiotic treatment, recovery, and post-CFPE baseline. Samples were treated with propidium monoazide prior to DNA extraction, to remove the impact of bacterial cell death artefacts following antibiotic treatment, and then characterised by 16S rRNA gene-targeted high-throughput sequencing. Partitioning CF microbiota into core and rare groups revealed compositional resistance to CFPE and resilience to antibiotics interventions. Mixed effects modelling of core microbiota members revealed no significant negative impact on the relative abundance of Pseudomonas aeruginosa across the exacerbation cycle. Our findings have implications for current CFPE management strategies, supporting reassessment of existing antimicrobial treatment regimens, as antimicrobial resistance by pathogens and other members of the microbiota may be significant contributing factors.

© 2014 . Background: Best practice when performing culture-independent microbiological analysis of sputum samples involves their rapid freezing and storage at -80 °C. However, accessing biobanked collections can mean that material has been passed through repeated freeze-thaw cycles. The aim of this study was to determine the impact of these cycles on microbial community profiles. Methods: Sputum was collected from eight adults with cystic fibrosis, and each sample was subjected to six freeze-thaw cycles. Following each cycle, an aliquot was removed and treated with propidium monoazide (PMA) prior to DNA extraction and 16S rRNA gene pyrosequencing. Results: The impact of freeze-thaw cycles was greatest on rare members of the microbiota, with variation beyond that detected with within-sample repeat analysis observed after three cycles. Conclusion: Four or more freeze thaw cycles result in a significant distortion of microbiota profiles from CF sputum.

Copyright © 2014 by the American Thoracic Society. Rationale: DNA-based microbiological studies are moving beyond studying healthy human microbiota to investigate diverse infectious diseases, including chronic respiratory infections, such as those in the airways of peoplewith cystic fibrosis (CF) and non-CF bronchiectasis. The species identified in the respiratory secretionmicrobiota fromsuch patients can be classified into those that are common and abundant among similar subjects (core) versus those that are infrequent and rare (satellite). This categorization provides a vital foundation for investigating disease pathogenesis and improving therapy. However, whether the core microbiota of people with different respiratory diseases, which are traditionally associated with specific culturable pathogens, are unique or shared with other chronic infections of the lower airways isnotwell studied. Little is also known about how these chronic infection microbiota change from childhood to adulthood. Objectives: We sought to compare the core microbiota in respiratory specimens from children and adults with different chronic lung infections. Methods: We used bacterial 16S rRNA gene pyrosequencing, phylogenetic analysis, and ecological statistical tools to compare the core microbiota in respiratory samples from three cohorts of symptomatic children with clinically distinct airway diseases (protracted bacterial bronchitis, bronchiectasis,CF), and from four healthy children.Wethen compared the core pediatric respiratory microbiota with those in samples from adults with bronchiectasis and CF. Measurements and Main Results: All three pediatric disease cohorts shared strikingly similar core respiratory microbiota that differed from adult CF and bronchiectasis microbiota. The most common species in pediatric disease cohort sampleswere also detected in those from healthy children. The adult CF and bronchiectasis microbiota also differed from each other, suggesting common early infecti

Spontaneously expectorated sputum is traditionally used as the sampling method for the investigation of lower airway infections. While guidelines exist for the handling of these samples for culture-based diagnostic microbiology, there is no comparable consensus on their handling prior to culture-independent analysis. The increasing incorporation of culture-independent approaches in diagnostic microbiology means that it is of critical importance to assess potential biases. The aim of this study was to assess the impact of delayed freezing on culture-independent microbiological analyses and to identify acceptable parameters for sample handling. Sputum samples from eight adult cystic fibrosis (CF) patients were collected and aliquoted into sterile Bijou bottles. Aliquots were stored at room temperature before being frozen at −80°C for increasing intervals, up to a 72-h period. Samples were treated with propidium monoazide to distinguish live from dead cells prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterize their bacterial compositions. Substantial variation was observed in samples with high-diversity bacterial communities over time, whereas little variation was observed in low-diversity communities dominated by recognized CF pathogens, regardless of time to freezing. Partitioning into common and rare species demonstrated that the rare species drove changes in similarity. The percentage abundance of anaerobes over the study significantly decreased after 12 h at room temperature (P = 0.008). Failure to stabilize samples at −80°C within 12 h of collection results in significant changes in the detected community composition.

This article rests in the context of the 2001 evaluation of Baltimore City Public School System’s (BCPSS) 5-year-old reform effort, conducted by Westat and its collaborators.2 In that context, the article describes findings on key human resource issues for the BCPSS. Briefly, the part of the evaluation on which this article is based was charged with appraising the success of efforts to improve the quality, stability, and effectiveness of the BCPSS instructional workforce (teachers and principals). The overall design of the evaluation, as well as findings in other key areas of the school system reform effort (e.g., governance and management, instruc-tional interventions, achievement outcomes) are described in the other articles that comprise this special issue. Four areas of the human resource effort are examined for both teachers and principals in the Baltimore City Public School System (BCPSS): (a) recruitment policies and practices, (b) mentoring and other retention strategies, (c) professional development, and (d) performance evaluation. Four methods of data gathering were used: one quantitative (survey), and three qualitative (document review, key informant interview, and focus group interview). These have been described elsewhere in this special issue, and will not be further detailed here.

This is the final annual report of a 4-year (1997-2001) third-party evaluation of the Structure of Intellect (SOI) Model Schools Pilot Program in Oregon. The SOI program was developed based on the learning theories and Structure of Intellect Model attributed to J. Guilford. The program used a combination of structured curriculum in the form of modules and an in-school SOI Learning Center to teach and develop learning abilities for elementary school students. This evaluation was approached from a systemic perspective that collected and examined relevant data from all Oregon schools using the SOI program and compared those to data from schools not using the program.The use of SOI classroom modules varied greatly among the pilot program schools, although it was apparent that the laboratory personnel who managed the program displayed kindness, dedication, and persistence. However, after 3 years of implementation for 15 schools and 3.5 years for 2 schools, the data collected from various sources and analyzed indicate no systemic or practical differences between the 17 SOI schools and their matched comparison schools. This conclusion, for academic achievement, rates of unacceptable student behavior or special education referrals, and student attendance was consistent over each of the 4 years. Nine appendixes contain additional information about the schools, materials used in the study, and data collection instruments.

What happens when evaluators use mixed methods to authenticate findings and policy makers, program producers, program staff, and program constituents place varying values on evidence of program effects? An external evaluation of the Structure of Intellect (SOI) Model Schools Pilot Program, mandated by the Oregon legislature for implementation in elementary schools since 1998, has produced findings from a multi-site, mixed-method program evaluation that illustrates this challenge. The ongoing charge of the evaluation is to address questions of student achievement, behavior, and special education referrals, based on the program's claims for improvement in those areas as a result of exposure to the SOI Program. This session will use the SOI evaluation to illustrate differences among stakeholders' views about the value of different sources of evidence. Additionally, we will suggest one systematic method for assigning value to each source of evidence that is both understandable and useful to policy makers, stakeholders, and evaluators.

This report presents findings of the third year evaluation of the Structure of Intellect (SOI) Model Schools Pilot Program in Oregon, a program based on the learning theories and Structure of Intellect model attributed to J. Guilford. The SOI program, developed by R. and M. Meeker, uses a combination of structured curriculum in the form of modules and an in-school SOI Learning Center to teach and develop important learning abilities for students. The SOI program focuses on 26 learning abilities claimed to be critical for effective learning. In 1999-2000, 17 elementary schools piloted the SOI program and 11 students served as case studies. As in the preceding 2 years, no systemic or practical differences were observed between the pilot schools and the 17 comparison schools included in the evaluation. No program effects have been observed in any of the key areas addressed by the evaluation. Careful synthesis of the data gathered for this evaluation does not support claims for school-wide improvements in academic achievement, reduction in referrals for special education services, reduction in referrals for inappropriate behavior, or improvements in school attendance rates. However, many program specialists and technicians believe that the program is effective in supporting student learning. It is possible that the individualized care students received through the SOI program has made considerable difference in their educational lives. The program has been extended for another year, and evaluation of the fourth year may detect some quantifiable differences in achievement for program participants. Nine appendixes contain supplemental information, teacher responses to study questions, and some data collection forms.

This report presents the findings of year 2 (July 1998-June 1999) of the third-party evaluation of the effectiveness of the Oregon Structure of Intellect (SOI) Model Schools Pilot Program, a program based on the learning theories and Structure of Intellect model attributed to J. Guilford. The SOI program, developed by R. and M. Meeker, uses a combination of structured curriculum in the form of modules and an in-school SOI Learning Center to teach and develop important learning abilities for students. The SOI program focuses on 26 learning abilities claimed to be critical for effective learning. In year 2, 19 elementary schools in Oregon participated in the SOI pilot program and evaluation. The evaluation also studied 19 comparison schools that did not participate in the SOI program. Data were collected through observation, surveys of staff, and qualitative evaluations through site visits. The evaluation focused heavily on the impact of the SOI program on students. In year 2, as in year 1, no measurable or easily identifiable benefits for students were detected. However, SOI specialists and technicians and most school administrators remained enthusiastic about the program, and most students seemed to enjoy the SOI Learning Center activities. Two-thirds of teachers surveyed believe that the SOI curriculum is helpful for student learning. Overall, the absence of SOI program effects, given the newness of the program and the difficulties of starting any new program, is not surprising. Some recommendations are made for increased accountability and program improvement. Ten appendixes contain supplemental information about the SOI schools, some materials used in the evaluation, information about survey respondents and focus groups, and some data collection forms.

No abstract available