Table 2 Comparison of targeted metagenomics and IS-Pro methods in terms of cost, time and ease of use in our setting
From: Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome
Description | Targeted metagenomics | IS-Pro method |
|---|---|---|
Laboratory cost per isolatea | $87.57(R 1Â 441.28) | $117.73 (R 1Â 937.85) |
Turnaround time (from DNA extraction till statistical analysis) | 9 days (user-dependent and platform-dependent) | 7 days |
Hands-on time (labour cost) | Laboratory: 5 days (1Â day for DNA extraction, 4 days for next-generation sequencing and clean-up) Analysis: 4 days (3 days for analysis using QIIME and 1Â day for statistical analysis) | Laboratory: 5 days (1Â day for DNA extraction, 1Â day for the IS-Pro PCR and 1Â day for clean-up and 2 days for sequencing) Analysis: 2 days (1Â day for analysis using IS-Pro proprietary software and 1Â day for statistical analysis) |
Steps involved | Bacterial DNA extraction PCR amplification of the target region Library preparation (and pooling of samples) Sequencing run Quality control analysis and generation of an OTU table using a program, such as QIIME2. Statistical analysis using a program, such as R | Bacterial DNA extraction PCR amplification using the IS-Pro kit Fragment analysis using a genetic analyser (uses capillary electrophoresis) Analysis of data and generation of an OTU table using IS-Pro proprietary software. Statistical analysis using a program, such as R |
Ease of use | Requires familiarity with Linux system | Easy to use (requires no prior knowledge of the IS-Pro propriety software) |