Stability of the human gut virome and effect of gluten-free diet.

Sanzhima Garmaeva,Alexandra Zhernakova,Colin Hill,Johanne E Spreckels,Thomas D.S Sutton,Jingyuan Fu,Lorraine A Draper,Cisca Wijmenga,Alexander Kurilshikov,Stephen R Stockdale,Bas E Dutilh,Andrey N Shkoporov,Trishla Sinha,Adam G Clooney,Anastasia Gulyaeva

doi:10.1016/j.celrep.2021.109132

Abstract

The human gut microbiome consists of bacteria, archaea, eukaryotes, and viruses. The gut viruses are relatively underexplored. Here, we longitudinally analyzed the gut virome composition in 11 healthy adults: its stability, variation, and the effect of a gluten-free diet. Using viral enrichment and a de novo assembly-based approach, we demonstrate the quantitative dynamics of the gut virome, including dsDNA, ssDNA, dsRNA, and ssRNA viruses. We observe highly divergent individual viral communities, carrying on an average 2,143 viral genomes, 13.1% of which were present at all 3 time points. In contrast to previous reports, the Siphoviridae family dominates over Microviridae in studied individual viromes. We also show individual viromes to be stable at the family level but to vary substantially at the genera and species levels. Finally, we demonstrate that lower initial diversity of the human gut virome leads to a more pronounced effect of the dietary intervention on its composition.

Highlights

The human gut microbiome has been linked to many diseases and conditions and is influenced by various host and environmental factors (Falony et al, 2016; Rothschild et al, 2018; Zhernakova et al, 2016)
As the stability of the gut virome under the influence of external factors is relatively underexplored, we aimed to study the effect of a gluten-free diet (GFD) on virome composition
Study design To determine the stability of the gut virome in response to dietary changes, we monitored the fecal viromes of 11 healthy adults who followed a GFD (Bonder et al, 2016)

Summary

Introduction

The human gut microbiome has been linked to many diseases and conditions and is influenced by various host and environmental factors (Falony et al, 2016; Rothschild et al, 2018; Zhernakova et al, 2016). Wide-scale studies of the gut virome are limited by multiple technical and methodological challenges (Garmaeva et al, 2019). Virome studies have far been performed on a relatively small scale. Despite these challenges, several studies have indicated the association of the gut virome with various diseases, including inflammatory bowel disease (Clooney et al, 2019; Norman et al, 2015), colorectal cancer (Nakatsu et al, 2018), type 1 and type 2 diabetes (Ma et al, 2018; Zhao et al, 2017), malnutrition (Reyes et al, 2015), acquired immune deficiency syndrome (Monaco et al, 2016), and Parkinson’s disease (Tetz et al, 2018). Successful treatment of Clostridium difficile-infected patients using fecal filtrate rather than full fecal microbiota transplant hints at a possible role for the virome and other filtrate components, such as the metabolome, in microbiome recovery after infection (Ott et al, 2017)

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