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. 2022 Feb 9;3(1):101170.
doi: 10.1016/j.xpro.2022.101170. eCollection 2022 Mar 18.

Protocol for the isolation, sequencing, and analysis of the gut phageome from human fecal samples

Shirley Bikel  1 , Luigui Gallardo-Becerra  1 , Fernanda Cornejo-Granados  1 , Adrian Ochoa-Leyva  1
Affiliations

Protocol for the isolation, sequencing, and analysis of the gut phageome from human fecal samples

Shirley Bikel et al. STAR Protoc. .

Abstract

The phage-bacteria interactions in the gut microbiome are critical for health and disease, but viruses of the human gut microbiome are poorly understood. Here, we present a simple and cost-efficient protocol for collecting viral-like particles (VLPs) from human fecal samples. We describe VLPs quantification using epifluorescence and TEM microscopy, followed by DNA sequencing and bioinformatics analysis. This protocol characterizes the gut phageome in normal-weight and obese children with metabolic syndrome. It is also suitable to conduct high-throughput studies for other diseases. For complete details on the use and execution of this profile, please refer to Bikel et al. (2021).

Keywords: Bioinformatics; Health Sciences; Metabolism; Microbiology; Microscopy; Molecular Biology; Sequence analysis; Sequencing; Systems biology.

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Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Microscopy visualization and counting of VLPs The image was modified from Bikel et al. (2021). (A) SYBR Green I-stained virus-like particles (VLPs) by epifluorescence microscopy. Red arrows show an example of the VLPs. The scale bar represents an approximate size of 10 µm. (B) TEM microscopy of VLPs. Red arrows show an example of the VLP morphology. The scale bar represents an approximate size of 0.5 µm.
Figure 2
Figure 2
DNA bioanalyzer graph of a purified Nextera library built with 1.5 ng of viral DNA
See this image and copyright information in PMC

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