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Fig. 1 | Microbiome

Fig. 1

From: Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

Fig. 1

Strategy for optimization of phage extractions protocols. Pre-processing (part 1) was used to remove and sediment large particles; purification (part 2) aimed to remove low molecular weight impurities and microbial cells. Boxes drawn with non-continuous lines represent steps that were not suitable for extraction of bacteriophages (heavy loss of spiked phages). Green-line boxes depict filthy or impure samples (particularly low molecular weight impurities, assessed by visual inspection and TEM). Blue-line boxes show pathways where ≥50 % of the population of spiked bacteriophages was lost. Purple-line boxes indicate presence of microbial cells. The optimization of procedures for purification started in routes 1 (for the PEG approach) and 6 (for the TFF approach). Throughout this optimization, the routes were diverged into new extraction routes (i.e., from route 1 to route 2) until the highest recovery rate of the spiked bacteriophages was reached. Route 6 represented the LIT protocol. Base on their efficiency, route 5 (PEG) and route 8 (TFF) became the optimized protocols

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