Stability of the Human Gut Virome and Effect of Gluten-Free Diet

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

doi:10.2139/ssrn.3677221

Sanzhima Garmaeva, Johanne E Spreckels + Show 13 more

Open Access

https://doi.org/10.2139/ssrn.3677221

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Abstract

The human gut microbiome is a complex ecosystem of bacteria, archaea, eukaryotes, and viruses. The composition and dynamics of the gut viruses, commonly termed the gut virome, are relatively underexplored. We performed a longitudinal analysis of the gut viral communities in 11 healthy adults in order to study individual variations, virome stability, and the effect of a gluten-free diet (GFD). 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 that individual’s viral communities are highly divergent, carrying on average 2,143 viral genomes, 13.1% of which were present at all time points. During the GFD, the virome was stable at the family level but showed substantial variation at the ranks of genera and species. Finally, we demonstrate that a lower initial viral diversity leads to a more pronounced effect of the dietary intervention.

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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