The lung in cystic fibrosis (CF) is home to numerous pathogens that shorten the lives of patients. The aim of the present study was to assess changes in the lung bacteriome following antibiotic therapy targeting Pseudomonas aeruginosa in children with CF. The study included nine children (9-18 years) with CF who were treated for their chronic or intermittent positivity for Pseudomonas aeruginosa. The bacteriomes were determined in 16 pairs of sputa collected at the beginning and at the end of a course of intravenous antibiotic therapy via deep sequencing of the variable region 4 of the 16S rRNA gene, and the total bacterial load and selected specific pathogens were assessed using quantitative real-time PCR. The effect of antipseudomonal antibiotics was observable as a profound decrease in the total 16S rDNA load (p = 0.001) as well as in a broad range of individual taxa including Staphylococcus aureus (p = 0.03) and several members of the Streptococcus mitis group (S. oralis, S. mitis, and S. infantis) (p = 0.003). Improvements in forced expiratory volume (FEV1) were associated with an increase in Granulicatella sp. (p = 0.004), whereas a negative association was noted between the total bacterial load and white blood cell count (p = 0.007). In conclusion, the data show how microbial communities differ in reaction to antipseudomonal treatment, suggesting that certain rare species may be associated with clinical parameters. Our work also demonstrates the utility of absolute quantification of bacterial load in addition to the 16S rDNA profiling.

• MeSH
• antibakteriální látky aplikace a dávkování   MeSH
• Bacteria klasifikace   účinky léků   genetika   izolace a purifikace   MeSH
• cystická fibróza farmakoterapie   mikrobiologie   MeSH
• dítě MeSH
• DNA bakterií genetika   MeSH
• lidé MeSH
• mikrobiota účinky léků   MeSH
• mladiství MeSH
• plíce mikrobiologie   MeSH
• pseudomonádové infekce farmakoterapie   mikrobiologie   MeSH
• Pseudomonas aeruginosa účinky léků   genetika   izolace a purifikace   fyziologie   MeSH
• RNA ribozomální 16S genetika   MeSH
• sputum mikrobiologie   MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

AIM: Current attempts to modulate the human microbiota and immune responses are based on probiotics or human-derived bacterial transplants. We investigated microbial modulation by soil and plant-based material. MATERIALS & METHODS: We performed a pilot study in which healthy adults were exposed to the varied microbial community of a soil- and plant-based material. RESULTS: The method was safe and feasible; exposure was associated with an increase in gut microbial diversity. CONCLUSION: If these findings are reproduced in larger studies nature-derived microbial exposure strategies could be further developed for testing their efficacy in the treatment and prevention of immune-mediated diseases.

• MeSH
• Bacteria klasifikace   genetika   izolace a purifikace   MeSH
• biodiverzita MeSH
• dospělí MeSH
• feces mikrobiologie   MeSH
• gastrointestinální trakt imunologie   mikrobiologie   MeSH
• imunita * MeSH
• imunomodulace MeSH
• kůže imunologie   mikrobiologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• pilotní projekty MeSH
• půda chemie   MeSH
• půdní mikrobiologie * MeSH
• rostliny mikrobiologie   MeSH
• střevní mikroflóra * MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• klinické zkoušky MeSH
• práce podpořená grantem MeSH

BACKGROUND: We set out to explore associations between the stool bacteriome profiles and early-onset islet autoimmunity, taking into account the interactions with the virus component of the microbiome. METHODS: Serial stool samples were longitudinally collected from 18 infants and toddlers with early-onset islet autoimmunity (median age 17.4 months) followed by type 1 diabetes, and 18 tightly matched controls from the Finnish Diabetes Prediction and Prevention (DIPP) cohort. Three stool samples were analyzed, taken 3, 6, and 9 months before the first detection of serum autoantibodies in the case child. The risk of islet autoimmunity was evaluated in relation to the composition of the bacteriome 16S rDNA profiles assessed by mass sequencing, and to the composition of DNA and RNA viromes. RESULTS: Four operational taxonomic units were significantly less abundant in children who later on developed islet autoimmunity as compared to controls-most markedly the species of Bacteroides vulgatus and Bifidobacterium bifidum. The alpha or beta diversity, or the taxonomic levels of bacterial phyla, classes or genera, showed no differences between cases and controls. A correlation analysis suggested a possible relation between CrAssphage signals and quantities of Bacteroides dorei. No apparent associations were seen between development of islet autoimmunity and sequences of yet unknown origin. CONCLUSIONS: The results confirm previous findings that an imbalance within the prevalent Bacteroides genus is associated with islet autoimmunity. The detected quantitative relation of the novel "orphan" bacteriophage CrAssphage with a prevalent species of the Bacteroides genus may exemplify possible modifiers of the bacteriome.

• MeSH
• autoimunita * MeSH
• autoimunitní nemoci krev   epidemiologie   etiologie   imunologie   MeSH
• Bacteroides klasifikace   imunologie   izolace a purifikace   virologie   MeSH
• bakteriální RNA chemie   metabolismus   MeSH
• bakteriofágy klasifikace   imunologie   izolace a purifikace   MeSH
• diabetes mellitus 1. typu krev   epidemiologie   etiologie   imunologie   MeSH
• dítě MeSH
• dysbióza imunologie   mikrobiologie   patofyziologie   virologie   MeSH
• feces mikrobiologie   virologie   MeSH
• fylogeneze MeSH
• kohortové studie MeSH
• Langerhansovy ostrůvky imunologie   MeSH
• lidé MeSH
• longitudinální studie MeSH
• molekulární typizace MeSH
• nemocnice univerzitní MeSH
• prospektivní studie MeSH
• riziko MeSH
• RNA ribozomální 16S chemie   metabolismus   MeSH
• RNA virová chemie   metabolismus   MeSH
• střevní mikroflóra imunologie   MeSH
• studie případů a kontrol MeSH
• výpočetní biologie MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• multicentrická studie MeSH
• Geografické názvy
• Finsko epidemiologie   MeSH

BACKGROUND: Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. RESULTS: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. CONCLUSIONS: The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

• MeSH
• genetická variace MeSH
• genomika metody   MeSH
• internet * MeSH
• lidé MeSH
• mikrobiota genetika   MeSH
• software * MeSH
• viry genetika   MeSH
• vysoce účinné nukleotidové sekvenování * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH