Abstract
To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showed significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. The contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.
Highlights
The impact of the mammalian gut microbiome on health and disease, especially its response to diet, has gained increasing attention in recent years
These gut bacterial communities have been shown to be resistant to dietary changes, recovering their preintervention structure once the host resumes a previously consumed diet (Zhang et al, 2012; David et al, 2013)
The relative abundances of Group II contigs are observed to share consistent trends in the baseline MF induced prophage (IND) samples, increasing in abundance on Day 1 relative to baseline Day 0 (1.8–3.9%, mean), decreasing in abundances after the diet disturbance (Day 22, 0.09%, mean) and increasing when returned to the baseline diet (Day 43, 8.8%, mean) (Supplementary Figure S7). These trends were not observed in the baseline MF VLP samples, where the majority of Unprecedented access to the gut microbiome through multiple targeted sequencing efforts Recent insights into the microbial processes and pathways that contribute to gut microbiome stability and resilience have focused on bacterial responses to diet in the gut system (Zhang et al, 2012; David et al, 2013)
Summary
(Breitbart et al, 2008; Reyes et al, 2010; Minot et al, 2011; Norman et al, 2015) and have been hypothesized to markedly alter bacterial community structure and function through gene exchange, eliminating niche competitors and modification of gene expression of hosts (Reyes et al, 2012; Duerkop et al, 2012; Barr et al, 2013). Short-term diet interventions have been shown to alter viral communities in humans (Minot et al, 2011), but the lasting impact of dietary shifts on viruses and gut health and their resistance to disturbances is unknown. Given their ability to markedly alter other ecosystems, there is reason to hypothesize that viruses are drivers of ecosystem function in the gut. Viruses in the stool were consumption (CDC, 2004) It is a high-saturated fat targeted in two separate fractions: virus-like particles diet (37.5% total kCal) and has previously been (VLPs) and inducible prophages (IND) present in gut shown to perturb the mouse intestinal microbiome bacteria. DNA isolation, extraction, and quantification methods are described in more detail in Supplementary Methods
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