ArticleBMC microbiology2021
Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome.
Article in BMC microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Comparison of microbiota profiles of fecal samples, rectal swabs and mucosal biopsies in patients with inflammatory bowel disease.Gut microbes reports · 2026Article
- Bacterial nitrite production oxidizes Fe(II) bioremediating acidic abandoned coal mine drainage.Applied and environmental microbiology · 2025Article
- Intratumoral microbiome: implications for immune modulation and innovative therapeutic strategies in cancer.Journal of biomedical science · 2025Review
- From bench to bedside: an interdisciplinary journey through the gut-lung axis with insights into lung cancer and immunotherapy.Frontiers in immunology · 2024Review
- Rapid Diagnostics of Joint Infections Using IS-Pro.Journal of clinical microbiology · 2023Article
- Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer.Frontiers in oncology · 2022Article
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Authors and funding
7 authors.
Funding
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Abstract
backgroundTargeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients.
methodsSpontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method.
resultsStatistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods' data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly.
conclusionsIt is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.
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