Gut dsDNA virome shows diversity and richness alterations associated with childhood obesity and metabolic syndrome

Abstract

Summary Changes in the human gut microbiome are associated with obesity and metabolic syndrome, but the role of the gut virome in both diseases remains largely unknown. We characterized the gut dsDNA virome of 28 school-aged children with healthy normal-weight (NW, n = 10), obesity (O, n = 10), and obesity with metabolic syndrome (OMS, n = 8), using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. The virome classification confirmed the bacteriophages' dominance, mainly composed of Caudovirales. Notably, phage richness and diversity of individuals with O and OMS tended to increase, while the VLP abundance remained the same among all groups. Of the 4,611 phage contigs composing the phageome, 48 contigs were highly prevalent in ≥80% of individuals, suggesting high inter-individual phage diversity. The abundance of several contigs correlated with gut bacterial taxa; and with anthropometric and biochemical parameters altered in O and OMS. To our knowledge, this gut phageome represents one of the largest datasets and suggests disease-specific phage alterations.

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

“…This protocol uses 0.212 × 0.212-millimeter images ( Figure 1 A).

Figure 1 Microscopy visualization and counting of VLPs The image was modified from Bikel et al. (2021 ).

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“…(2020) ; it is not essential for virome studies. Note: The sample used in this protocol was previously reported in the Bikel et al. (2021) study.…”

“…FC-131-1024 Bioanalyzer High Sensitivity DNA Analysis Agilent Technologies Cat. 5067-4626 Deposited data Assembled contigs ( Bikel et al., 2021 ) BioProject PRJNA646512 BioSample SAMN15545081 In-house scripts describing the data analysis process ( Bikel et al., 2021 ) https://github.com/lab8a/2021-iScience-Phageome ; in Zenodo at https://doi.org/10.5281/zenodo.5846703 . Software and algorithms FastQC The Babraham Institute https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Trim Galore 1.12 The Babraham Institute https://github.com/FelixKrueger/TrimGalore Fastx Toolkit 0.7 Hannon Lab http://hannonlab.cshl.edu/fastx_toolkit/index.html CD-HIT 4.6 ( Fu et al., 2012 ) http://cd-hit.org/ R 3.6.2 N/A https://www.r-project.org/ IDBA-UD assembler 1.1.1 ( Peng et al., 2012 ) https://i.cs.hku.hk/∼alse/hkubrg/projects/idba_ud/ Bowtie 2.3.5 ( Langmead and Salzberg, 2012 ) http://bowtie-bio.sourceforge.net/bowtie2/index.shtml VirSorter 2.2.1 ( Guo et al., 2021 ) https://github.com/jiarong/VirSorter2 QIIME 1.9 ( Caporaso et al., 2010 ) …”

“…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) .…”

“…For complete details on the use and execution of this profile, please refer to Bikel et al. (2021) .…”