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

Shirley Bikel; Luigui Gallardo-Becerra; Fernanda Cornejo-Granados; Adrian Ochoa-Leyva

doi:10.1016/j.xpro.2022.101170

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

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

Authors

Shirley Bikel¹, Luigui Gallardo-Becerra¹, Fernanda Cornejo-Granados¹, Adrian Ochoa-Leyva¹

Affiliation

¹ Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Child
Feces / microbiology
Gastrointestinal Microbiome* / genetics
Humans
Pediatric Obesity*
Sequence Analysis, DNA
Virome