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"secondary-accession": "SRP110811",
"centre-name": "University of Pennsylvania",
"public-release-date": null,
"study-abstract": "To determine if any microbes are enriched in sarcoidosis relative to healthy controls. 16S, ITS tagged sequencing; shotgun sequencing; viral purification and sequencing.",
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"secondary-accession": "SRP425510",
"centre-name": "University of Pittsburgh",
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"study-abstract": "A re-sequencing of Lung HIV Microbiome Project (LHMP) BAL/OW/IS gDNA samples on the Illumina MiSeq platform using the V4 Caporaso primer set.",
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"last-update": "2023-09-26T10:31:21",
"secondary-accession": "SRP135694",
"centre-name": "University of Toronto",
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"study-abstract": "The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq): a method for deep sequencing of the bacterial 16S rRNA gene using next-generation sequencing technology. SI-Seq serially sequences portions of the V5, V6 and V7 hypervariable regions from barcoded 16S rRNA amplicons using an Illumina short-read genome analyzer. SI-Seq obtains taxonomic resolution similar to 454 pyrosequencing for a fraction of the cost, and can produce hundreds of thousands of reads per sample even with very high multiplexing. We validated SI-Seq using single species and mock community controls, and via a comparison to cystic fibrosis lung microbiota sequenced using 454 FLX Titanium. Our control runs show that SI-Seq has a dynamic range of at least five orders of magnitude, can classify >96% of sequences to the genus level, and performs just as well as 454 and paired-end Illumina methods in estimation of standard microbial ecology diversity measurements. We illustrate the utility of SI-Seq in a pilot sample of central airway secretion samples from cystic fibrosis patients.",
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"secondary-accession": "SRP216282",
"centre-name": "University of Washington",
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"study-abstract": "Immunocompromised patients are at increased risk for pneumonia. Standard microbiological culture may fail to identify unusual or unexpected organisms; culture-independent methods have improved our ability to deconvolute polymicrobial patient samples. We hypothesized that a more complete assessment of the microbial composition of bronchoalveolar lavage (BAL) samples would identify changes to routine clinical laboratory procedures that improve pathogen recovery. 20 consecutive BAL samples from oncology or transplant patients were plated to three standard and four additional media, and cultivable bacteria present were identified by next-generation 16S rRNA gene sequencing (NGS16S) analysis of DNA extracted from washed culture plates. NGS16S analysis was also performed on DNA extracted directly from patient samples. 96% of all organisms identified were cultivable, but only 21% were reported by standard culture, indicating that standard work-up can be further optimized. Direct NGS16S correlated well with standard culture results, identifying the same predominant organism in 50% of samples. When different predominant organisms were identified, NGS16S most often detected anaerobes, whose growth is unsupported by standard culture conditions. Brucella agar was the best single value-added media, supporting the growth of the largest number of organisms for the most specimens. Anaerobes are underappreciated BAL constituents. NGS16S identifies more organisms per sample and allows identification of fastidious organisms, while culture is better at capturing organisms when bacterial load is low, and allows incidental recovery of non-bacterial pathogens such as yeast or molds. Molecular and culture-based methods together detect more relevant organisms in clinical samples than either method alone.",
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"secondary-accession": "SRP201083",
"centre-name": "University of Dundee",
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"study-abstract": "Microbiome sequencing of induced sputum samples from patients with COPD, Bronchiectasis or COPD and Bronchiectasis taking during periods of disease stability and during exacerbations.",
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"last-update": "2023-09-25T23:17:38",
"secondary-accession": "SRP214694",
"centre-name": "University of Pittsburgh",
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"study-abstract": "Metagenomic sequencing of respiratory microbial communities for etiologic pathogen identification in pneumonia may help overcome the limitations of current culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore sequencing for severe pneumonia diagnosis. We conducted a case-control study of mechanically-ventilated patients with and without pneumonia. We collected endotracheal aspirate samples (ETAs) and applied a microbial DNA enrichment method prior to performing metagenomic sequencing with the Oxford Nanopore MinION device. We compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing. We demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive clinical cultures and insights into the composition of culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes.",
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"last-update": "2023-09-25T23:03:51",
"secondary-accession": "SRP213919",
"centre-name": "University of Michigan",
"public-release-date": null,
"study-abstract": "The goal of this project was to determine the relationship between lung microbiota and clinical outcomes in critically ill patients. Miniature bronchoalveolar lavage was performed within 24 hours of admission on critically ill patients receiving mechanical ventilation. Bacterial communities were characterized using 16S rRNA gene amplicon sequencing using the Illumina MiSeq platform.",
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"last-update": "2023-09-25T21:18:21",
"secondary-accession": "ERP105190",
"centre-name": "NORTHUMBRIA UNIVERSITY, NEWCASTLE",
"public-release-date": null,
"study-abstract": "Exhaled breath condensate is a promising way in identifying biomarkers of lung disease but the current devices used have disadvantages. The EcoScreen has the disadvantage of not being portable and the R-Tube cannot efficiently keep the sample cool. A 'prototpye' was been created to alleviate these issues. With the 'prototype', EBC samples were taken and files were concatenated together with md5 checksums allowing for data verification. Data was uploaded and results were compared to current type of collection devices.",
"study-name": "The Investigation and Analysis of Microbiomic Data Relating to Diseases Surrounding the Deep Lung Tissue",
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"type": "studies",
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"last-update": "2023-09-25T21:14:04",
"secondary-accession": "SRP188475",
"centre-name": "University of Washington",
"public-release-date": null,
"study-abstract": "Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. Additionally, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. This study describes a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. This method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance, underscoring the substantial impact of DNA from sources other than live bacteria in microbiological analyses of complex, chronic infection specimens.",
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"last-update": "2023-09-25T21:10:40",
"secondary-accession": "SRP122946",
"centre-name": "Minneapolis VA",
"public-release-date": null,
"study-abstract": "The rationale for the present study is that evaluation of the pathogenic character of the COPD lung microbiota has been hindered by concerns that oral taxa found in the COPD lung microbiota are the result of sample contamination rather than aspiration. Therefore, we have designed the present study to sample the mild or moderate COPD lung tissue microbiota surgically—without passing the sample through the oropharynx—and avoiding potential upper airway contamination of lung samples. Demonstrating that oral microbes are true components of the COPD lung microbiota will implicate aspiration as a potential pathogenic mechanism in COPD. We hypothesized that oral bacteria are true members of the early-stage COPD lung microbiota and exhibit ecologic drift.",
"study-name": "16S sequencing from human airway sites Raw sequence reads",
"data-origination": "HARVESTED"
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