ArticleMultidisciplinary respiratory medicine2019
Comparison of different conditions for DNA extraction in sputum - a pilot study.
Article in Multidisciplinary respiratory medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT04557215 (Evaluation of the Efficacy and Safety of Rifaximin in Combination With N-acetylcysteine), which is not on this map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Evaluation of the Efficacy and Safety of Rifaximin in Combination With N-acetylcysteine (NAC) in Adult Patients With Irritable Bowel Syndrome With Diarrhea
Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Beyond just correlation: causal machine learning for the microbiome, from prediction to health policy with econometric tools.Frontiers in microbiology · 2025Pooled it
- Metrological evaluation of DNA extraction method effects on the bacterial microbiome and resistome in sputum.mSystems · 2024Article
- Pro-resolving and pro-inflammatory fatty acid-derived mediators in sputum of stable state bronchiectasis patients.Respiratory research · 2022Observational
- Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies.Microbiology spectrum · 2022Article
- Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies.Genomics, proteomics & bioinformatics · 2022Article
- Prevalence and serotyping of S. pneumoniae in a large vaccine-naive cohort of adults with cystic fibrosis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2021Observational
- The biology of pulmonary exacerbations in bronchiectasis.European respiratory review : an official journal of the European Respiratory Society · 2019Review
- Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study.BMC microbiology · 2019Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe analysis of microbiome in respiratory samples is a topic of great interest in chronic respiratory diseases. The method used to prepare sputum samples for microbiome analysis is very heterogeneous. The selection of the most suitable methodology for DNA extraction is fundamental to have the most representative data. The objective of this study was to compare different conditions for DNA extraction from sputum in adult patients with bronchiectasis.
methodsFive sputum samples from bronchiectasis patients were collected at the Policlinico Hospital in Milan, Italy. Eighteen conditions for DNA extraction were compared, including two enzyme-based (Roche and Zymo) and one beads-based (Mobio) technique. These techniques were tested with/without Dithiothreitol (DTT) and with/without lysostaphin (0.18 and 0.36 mg/mL) step. DNA was quantified, tested using Real-time PCR for 16S rDNA and
resultsAlthough 16S rDNA was similarly detected across all the different techniques, Roche kit gave the highest DNA yield. The lowest Ct values for Real-time PCR for
conclusionsNone of the conditions emerged to be superior to the others even if enzyme-based kits seem to be needed in order to have a higher extraction yield.
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