46 research outputs found

    Persistent intestinal abnormalities and symptoms in cystic fibrosis: The underpinning mechanisms impacting gut health and motility. Protocol for a systematic review.

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    Background Patients with cystic fibrosis (CF) are characterised by abnormalities of the intestinal tract relating to gut motility and physiological issues, with daily symptoms of disease including abdominal pain, flatulence, bloating, and constipation. With improvements in respiratory outcomes, a shift in disease manifestations has highlighted the prevalence of the gastrointestinal-related problems associated with CF, yet most therapies currently in clinical use for the gut symptoms of CF have been repurposed from other disease indications and have not been developed with a knowledge of the mechanisms underpinning gastrointestinal disease in CF. Increased attention towards the role of intestinal inflammation and microbial dysbiosis in the CF population warrants a comprehensive knowledge of these aspects alongside the increased luminal fat content, dysmotility, and small intestinal bacterial overgrowth (SIBO) resultant of the primary consequences of CFTR dysfunction (disrupted fluid secretion and pancreatic insufficiency), and how they contribute towards the intestinal complications of CF disease. Methods and Study Design We will conduct a systematic review to comprehensively address our current understanding of the primary consequences of CFTR dysfunction, and their subsequent secondary effects that contribute towards the disruption of gut motility, health, and associated symptoms in the CF intestine. Databases searched will include PubMed, CINAHL, MEDLINE and the Cochrane library from 1939 until a specified date of last search, alongside clinical trial databases for ongoing studies. Search strategies will include various terminology that relates to the primary mechanistic defects of CF, postulated secondary effects of such defects, and symptoms experienced in patients. A full search strategy is outlined in Appendix B. One reviewer will apply an inclusion criterion to obtained abstracts. Following agreement from a second reviewer, full-text articles will be sought, and data will be extracted from relevant articles. Disagreements will be resolved with a third reviewer. The quality of data will be assessed by the GRADE criteria. Data will be used to present a narrative, and where possible, quantitative synthesis. Discussion This systematic review will discuss our current understanding of the underpinning mechanisms of the persisting abnormalities in gut health and motility within CF, addressing potential intricate relationships that further contribute to disease progression within the intestinal tract. Furthermore, we will identify current gaps in the literature to propose directions for future research. A comprehensive understanding of these aspects in relation to intestinal abnormalities will aid future clinical directions

    Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses

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    © 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

    Siblings of patients with Crohn's disease exhibit a biologically relevant dysbiosis in mucosal microbial metacommunities

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    © 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

    Spatial and temporal variability in the potential of river water biofilms to degrade p-nitrophenol

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    © 2016 Elsevier Ltd In order to predict the fate of chemicals in the environment, a range of regulatory tests are performed with microbial inocula collected from environmental compartments to investigate the potential for biodegradation. The abundance and distribution of microbes in the environment is affected by a range of variables, hence diversity and biomass of inocula used in biodegradation tests can be highly variable in space and time. The use of artificial or natural biofilms in regulatory tests could enable more consistent microbial communities be used as inocula, in order to increase test consistency. We investigated spatial and temporal variation in composition, biomass and chemical biodegradation potential of bacterial biofilms formed in river water. Sampling time and sampling location impacted the capacity of biofilms to degrade p-nitrophenol (PNP). Biofilm bacterial community structure varied across sampling times, but was not affected by sampling location. Degradation of PNP was associated with increased relative abundance of Pseudomonas syringae. Partitioning of the bacterial metacommunity into core and satellite taxa revealed that the P. syringae could be either a satellite or core member of the community across sampling times, but this had no impact on PNP degradation. Quantitative PCR analysis of the pnpA gene showed that it was present in all samples irrespective of their ability to degrade PNP. River biofilms showed seasonal variation in biomass, microbial community composition and PNP biodegradation potential, which resulted in inconsistent biodegradation test results. We discuss the results in the context of the mechanisms underlying variation in regulatory chemical degradation tests

    Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention

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    © 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

    Predominant pathogen competition and core microbiota divergence in chronic airway infection

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    © 2015 International Society for Microbial Ecology All rights reserved. Chronic bacterial lung infections associated with non-cystic fibrosis bronchiectasis represent a substantial and growing health-care burden. Where Pseudomonas aeruginosa is the numerically dominant species within these infections, prognosis is significantly worse. However, in many individuals, Haemophilus influenzae predominates, a scenario associated with less severe disease. The mechanisms that determine which pathogen is most abundant are not known. We hypothesised that the distribution of H. influenzae and P. aeruginosa would be consistent with strong interspecific competition effects. Further, we hypothesised that where P. aeruginosa is predominant, it is associated with a distinct 'accessory microbiota' that reflects a significant interaction between this pathogen and the wider bacterial community. To test these hypotheses, we analysed 16S rRNA gene pyrosequencing data generated previously from 60 adult bronchiectasis patients, whose airway microbiota was dominated by either P. aeruginosa or H. influenzae. The relative abundances of the two dominant species in their respective groups were not significantly different, and when present in the opposite pathogen group the two species were found to be in very low abundance, if at all. These findings are consistent with strong competition effects, moving towards competitive exclusion. Ordination analysis indicated that the distribution of the core microbiota associated with each pathogen, readjusted after removal of the dominant species, was significantly divergent (analysis of similarity (ANOSIM), R=0.07, P=0.019). Taken together, these findings suggest that both interspecific competition and also direct and/or indirect interactions between the predominant species and the wider bacterial community may contribute to the predominance of P. aeruginosa in a subset of bronchiectasis lung infections

    Bacterial Signatures of Paediatric Respiratory Disease : An Individual Participant Data Meta-Analysis

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    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 (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.Peer reviewe

    Lung function and microbiota diversity in cystic fibrosis

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    Abstract: Background: Chronic infection and concomitant airway inflammation is the leading cause of morbidity and mortality for people living with cystic fibrosis (CF). Although chronic infection in CF is undeniably polymicrobial, involving a lung microbiota, infection surveillance and control approaches remain underpinned by classical aerobic culture-based microbiology. How to use microbiomics to direct clinical management of CF airway infections remains a crucial challenge. A pivotal step towards leveraging microbiome approaches in CF clinical care is to understand the ecology of the CF lung microbiome and identify ecological patterns of CF microbiota across a wide spectrum of lung disease. Assessing sputum samples from 299 patients attending 13 CF centres in Europe and the USA, we determined whether the emerging relationship of decreasing microbiota diversity with worsening lung function could be considered a generalised pattern of CF lung microbiota and explored its potential as an informative indicator of lung disease state in CF. Results: We tested and found decreasing microbiota diversity with a reduction in lung function to be a significant ecological pattern. Moreover, the loss of diversity was accompanied by an increase in microbiota dominance. Subsequently, we stratified patients into lung disease categories of increasing disease severity to further investigate relationships between microbiota characteristics and lung function, and the factors contributing to microbiota variance. Core taxa group composition became highly conserved within the severe disease category, while the rarer satellite taxa underpinned the high variability observed in the microbiota diversity. Further, the lung microbiota of individual patient were increasingly dominated by recognised CF pathogens as lung function decreased. Conversely, other bacteria, especially obligate anaerobes, increasingly dominated in those with better lung function. Ordination analyses revealed lung function and antibiotics to be main explanators of compositional variance in the microbiota and the core and satellite taxa. Biogeography was found to influence acquisition of the rarer satellite taxa. Conclusions: Our findings demonstrate that microbiota diversity and dominance, as well as the identity of the dominant bacterial species, in combination with measures of lung function, can be used as informative indicators of disease state in CF. BBFJdPr3cu-jH3LTAhe361Video Abstrac
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