Abstract Background Fungal involvement in asthma is associated with severe disease. The full spectrum of fungal species in asthma is not well described and is derived largely from insensitive culture techniques. Objectives To use high‐throughput sequencing to describe the airway mycobiota in asthmatics with and without fungal sensitization and healthy controls; to compare samples representing different airway compartments; to determine whether the mycobiota was influenced by the fungal composition of outdoor air; and to compare findings with clinically relevant outcomes. Methods We amplified the internal transcribed spacer region 2 of the nuclear ribosomal operon to identify the fungal species present. Ninety‐seven subjects were recruited and provided sputum (83 asthmatics; 14 healthy subjects), with 29 also undergoing a bronchoscopy. A subset of airway samples were compared with matched outdoor air and mouthwash samples. Results Two hundred and six taxa at the species level were identified in sputum, most at low relative abundance. Aspergillus fumigatus , Candida albicans and Mycosphaerella tassiana had the highest relative abundances and were the most prevalent species across all subjects. The airway mycobiota consisted of a complex community with high diversity between individuals. Notable shifts in the balance of fungi detected in the lung were associated with asthma status, asthma duration and biomarkers of inflammation. Aspergillus tubingensis , a member of the Aspergillus niger species complex, was most prevalent from bronchoscopic protected brush samples and significantly associated with a low sputum neutrophilia. Cryptococcus pseudolongus , from the Cryptococcus humicola species complex, was more abundant from bronchoscopy samples than sputum, and differentially more abundant in asthma than health. Conclusions and Clinical Relevance The airway mycobiota was dominated by a relatively small number of species, but was distinct from the oropharyngeal mycobiota and air samples. Members of the A. niger and C. humicola species complexes may play unexpected roles in the pathogenesis of asthma.
Increasing use of fish feed containing the chitin synthesis inhibiting anti-parasitic drug diflubenzuron (DFB) in salmon aquaculture has raised concerns over its impact on coastal ecosystems. Larvae of Northern shrimp (Pandalus borealis) were exposed to DFB medicated feed under Control conditions (7.0 °C, pH 8.0) and under Ocean Acidification and Warming conditions (OAW, 9.5 °C and pH 7.6). Two weeks' exposure to DFB medicated feed caused significantly increased mortality. The effect of OAW and DFB on mortality of shrimp larvae was additive; 10% mortality in Control, 35% in OAW, 66% in DFB and 92% in OAW + DFB. In OAW + DFB feeding and swimming activity were reduced for stage II larvae and none of the surviving larvae developed to stage IV. Two genes involved in feeding (GAPDH and PRLP) and one gene involved in moulting (DD9B) were significantly downregulated in larvae exposed to OAW + DFB relative to the Control. Due to a shorter intermoult period under OAW conditions, the OAW + DFB larvae were exposed throughout two instead of one critical pre-moult period. This may explain the more serious sub-lethal effects for OAW + DFB than DFB larvae. A single day exposure at 4 days after hatching did not affect DFB larvae, but high mortality was observed for OAW + DFB larvae, possibly because they were exposed closer to moulting. High mortality of shrimp larvae exposed to DFB medicated feed, indicates that the use of DFB in salmon aquaculture is a threat to crustacean zooplankton.
Introduction: Airway colonisation with Aspergillus fumigatus increases with age in CF, however its significance in lung disease progression remains uncertain. Molecular methods provide a dynamic approach in characterising the CF airway microbiome in relation to fungal culture (FC) positivity. Objectives: To characterise the change in bacterial and fungal microbiota in relation to fungal airway colonisation. Methods: A prospective, single-centre longitudinal study over a six-year period, including paediatric and adult CF patients. Annual spontaneous and induced sputum samples were collected. Results: Seventy patients provided 235 respiratory samples. Median age at recruitment was 17 years (range 0.5–59 years) with a median percent predicted FEV1 of 88% (range 26–135%). 60% of participants were FC positive, of which 3% were persistently colonised. 68% of the FC naïve group were aged <15 years. FC positivity was independently associated with reduced bacterial diversity. Streptococcus and Pseudomonas were the predominant taxa across both FC groups. Rare bacterial and fungal taxa were more abundant within the FC negative cohort. Participants with persistent fungal airway colonisation displayed differences in bacterial and fungal community structure, and demonstrated a steeper decline in fungal diversity over time. This cohort also demonstrated a predominance of Candida paraspsilosis, C. albicans and A. fumigatus. Conclusion: Chronic Aspergillus fumigatus airway colonisation is associated with a change in bacterial and fungal community structure and diversity in CF. Further comparative studies are needed to understand the impact of fungal airway colonisation on the post modulator CF airway microbiome.
Interferons (IFNs) are cytokines that have proinflammatory, antiviral, and immunomodulatory effects and play a central role during a host response to pathogens. The IFN family contains both type I and type II molecules. While there are a number of type I IFNs, there is only one type II IFN. Recently both type I and type II IFN genes have been cloned in salmonid fish and recombinant proteins produced showing IFN activity. We have stimulated an Atlantic salmon cell line (SHK-1) with both type I and type II recombinant salmonid IFNs and analyzed the transcriptional response by microarray analysis. Cells were exposed to recombinant IFNs for 6 or 24 h or left unexposed as controls. RNA was hybridized to an Atlantic salmon cDNA microarray (salmon 17K feature TRAITS/SGP array) in order to assess differential gene expression in response to IFN exposure. For IFN I and II, 47 and 72 genes were stimulated, respectively; most genes were stimulated by a single IFN type, but some were affected by both IFNs, indicating coregulation of the IFN response in fish. Real-time PCR analysis was employed to confirm the microarray results for selected differentially expressed genes in both a cell line and primary leukocyte cultures.
Additional file 1: All transcripts differentially expressed more than twofold (p < 0.05) relative to C early in each moult cluster group. Each sheet in the file lists transcripts that were differentially expressed more than twofold (B&H adjusted p < 0.05) relative to C early for each moult cluster group. Each transcript is listed with GenBank accession number, contig/singleton identifier, top BLAST (E < 1e-5) description (tBLASTX hits are underlined, all others are BLASTX), E value of the BLAST hit, Gene Ontology identifiers (C = cellular component, F = molecular function, P = biological process), Pfam protein domain (E < 1e-5), fold change (with inverted fold change for down regulated transcripts) and false discovery rate adjusted p value. (XLS 272 KB)
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