Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut

Abstract

Bacterial viruses (phages) are the most abundant biological group on Earth and are more genetically diverse than their bacterial prey/ hosts. To characterize their role as agents shaping gut microbial community structure, adult germ-free mice were colonized with a consortium of 15 sequenced human bacterial symbionts, 13 of which harbored one or more predicted prophages. One member, Bacteroides cellulosilyticus WH2, was represented by a library of isogenic transposon mutants that covered 90% of its genes. Once assembled, the community was subjected to a staged phage attack with a pool of live or heat-killed virus-like particles (VLPs) purified from the fecal microbiota of five healthy humans. Shotgun sequencing of DNA from the input pooled VLP preparation plus shotgun sequencing of gut microbiota samples and purified fecal VLPs from the gnotobiotic mice revealed a reproducible nonsimultaneous pattern of attack extending over a 25-d period that involved five phages, none described previously. This system allowed us to (i) correlate increases in specific phages present in the pooled VLPs with reductions in the representation of particular bacterial taxa, (ii) provide evidence that phage resistance occurred because of ecological or epigenetic factors, (iii) track the origin of each of the five phages among the five human donors plus the extent of their genome variation between and within recipient mice, and (iv) establish the dramatic in vivo fitness advantage that a locus within a B. cellulosilyticus prophage confers upon its host. Together, these results provide a defined community-wide view of phage-bacterial host dynamics in the gut.T he human gut is home to tens of trillions of microbial cells representing all three domains of life, although most are bacteria. These organisms collaborate and compete for functional niches and physical locations (habitats). Together, they form a continuously functioning microbial metabolic "organ." The microbial diversity, interpersonal variation, and dynamism of the human gut microbiota make the task of identifying the factors that define community configurations extremely challenging.In some ecosystems, phages maintain high bacterial strain level diversity through lysis of their host strains (constant diversity dynamics model; refs 1, 2). The resulting emptied niche is filled with either an evolved resistant bacterial strain or a taxonomically closely related bacterial species. These dynamics have been observed in open marine environments (1). In contrast, a recent study of 37 healthy adults indicated that a person's fecal microbiota was remarkably stable, with 60% of bacterial strains retained over the course of 5 y (3). Stability followed a power law dynamic that when extrapolated suggests that most strains in an individual's gut community are retained for decades (3). In a metagenomic analysis of virus-like particles (VLPs) purified from the fecal microbiota of healthy adult monozygotic twins and their mothers, sampled over the course of a year, viral community structure exh...

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

“…We acknowledge the fact that miBC is not an exhaustive collection; important bacterial taxa are still missing (for example, segmented filamentous bacteria or species of the phyla TM7 and Deferribacteres) and other microorganisms such as fungi and archaea, as well as viruses, are also important to investigate 39,40 . Moreover, key metabolic functions such as the conversion of bile acids require more detailed investigation.…”

Healthy human gut phageome

“…The dynamics that arise from a lytic-lysogenic balance in the gut are still unknown. However, the active gut bacteriophages have been shown to influence bacterial population dynamics in a murine gut microbial ecosystem model (20), and to confer advantages to certain microbiome members during stress, such as antibiotic exposure (21). We presume that the active phageome of healthy people plays a critical role in maintaining the structure and function of a healthy gut ecosystem.…”

“…On one hand, there is evidence of more phageome similarity among relatives and household members compared with unrelated individuals (7,8). On the other hand, there is evidence that some phages are common to unrelated people (13,19,20,22). Stern et al (19) identified 991 bacteriophage sequences from cellular metagenomes that were shared across 124 individuals.…”

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

“…Studies involving deliberate introduction of purified human fecal VLP preparations into gnotobiotic mice colonized with a defined consortium of sequenced members of the human gut microbiota have shown that viral-bacterial dynamics in vivo are complex; the correlations between phage and bacterial strain abundances are not always obvious and involve negative correlations shifted in time as a result of a predator-prey dynamic, whereas prophages have linear positive correlations (35). As a consequence, answering this question promises to be challenging.…”