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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 1 441.28) $117.73 (R 1 937.85)
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 (1 day for DNA extraction, 4 days for next-generation sequencing and clean-up)
Analysis: 4 days (3 days for analysis using QIIME and 1 day for statistical analysis)
Laboratory: 5 days (1 day for DNA extraction, 1 day for the IS-Pro PCR and 1 day for clean-up and 2 days for sequencing)
Analysis: 2 days (1 day for analysis using IS-Pro proprietary software and 1 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)
  1. aThe cost is the cost at the time the study was conducted, is depicted in South African Rand and is dependent on international exchange rates (the cost in the dollar was based on the exchange rate on 04/10/2020)