ArticleScientific reports2020
Optimized DNA extraction and purification method for characterization of bacterial and fungal communities in lung tissue samples.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 31 citations in OpenAlex.
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- Combination of Sample Preservation Approaches and DNA Extraction Methods for Long-Read Sequencing of Nudibranchs' Genomes.Ecology and evolution · 2025Article
- The Microbiota of the Outer Gut Mucus Layer of the Migrating Northeast Arctic Cod (Microorganisms · 2024Article
- Optimization of lung tissue pre-treatment by bead homogenization for subsequent culturomics.Scientific reports · 2024Article
- Evaluation of different DNA extraction methods based on steel-bullet beating for molecular diagnosis of onychomycosis.Journal of clinical laboratory analysis · 2022Article
- Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels.Frontiers in microbiology · 2022Review
- An optimized approach for processing of frozen lung and lavage samples for microbiome studies.PloS one · 2022Article
- Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage.Cell host & microbe · 2021Article
- Gut microbiota genome features associated with brain injury in extremely premature infants.Gut microbesArticle
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
Abstract
Human lungs harbor a scarce microbial community, requiring to develop methods to enhance the recovery of nucleic acids from bacteria and fungi, leading to a more efficient analysis of the lung tissue microbiota. Here we describe five extraction protocols including pre-treatment, bead-beating and/or Phenol:Chloroform:Isoamyl alcohol steps, applied to lung tissue samples from autopsied individuals. The resulting total DNA yield and quality, bacterial and fungal DNA amount and the microbial community structure were analyzed by qPCR and Illumina sequencing of bacterial 16S rRNA and fungal ITS genes. Bioinformatic modeling revealed that a large part of microbiome from lung tissue is composed of microbial contaminants, although our controls clustered separately from biological samples. After removal of contaminant sequences, the effects of extraction protocols on the microbiota were assessed. The major differences among samples could be attributed to inter-individual variations rather than DNA extraction protocols. However, inclusion of the bead-beater and Phenol:Chloroform:Isoamyl alcohol steps resulted in changes in the relative abundance of some bacterial/fungal taxa. Furthermore, inclusion of a pre-treatment step increased microbial DNA concentration but not diversity and it may contribute to eliminate DNA fragments from dead microorganisms in lung tissue samples, making the microbial profile closer to the actual one.
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