Healthy human gut phageome

Abstract

The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of humans, we analyzed a deep DNA sequence dataset of active bacteriophages and available metagenomic datasets of the gut bacteriophage community from healthy individuals. We found 23 shared bacteriophages in more than one-half of 64 healthy individuals from around the world. These shared bacteriophages were found in a significantly smaller percentage of individuals with gastrointestinal/irritable bowel disease. A network analysis identified 44 bacteriophage groups of which 9 (20%) were shared in more than one-half of all 64 individuals. These results provide strong evidence of a healthy gut phageome (HGP) in humans. The bacteriophage community in the human gut is a mixture of three classes: a set of core bacteriophages shared among more than one-half of all people, a common set of bacteriophages found in 20-50% of individuals, and a set of bacteriophages that are either rarely shared or unique to a person. We propose that the core and common bacteriophage communities are globally distributed and comprise the HGP, which plays an important role in maintaining gut microbiome structure/function and thereby contributes significantly to human health.

Keywords: gut microbiome bacteriophage; gut microbiome viruses; human gut viral metagenome; shared microbiome viruses.

Fig. S1.

Bacteriophage community abundance distribution (A and B, individual 1; C and D, individual 2). (Left) Relative abundance of the most abundant bacteriophages (10–0.1% range) in the gut of study individuals. (Right) Percentage of normalized reads that are recruited to percentage of contigs shown in different abundance ranges of the community. On average, 7% of the bacteriophage contigs in each community account for 91% of the normalized reads, showing that a minority of the bacteriophage species dominates the bacteriophage community.

Fig. S2.

Percentage of bacteriophages present in more than 20% of healthy individuals. A total of 62 healthy individuals from three cohorts around the world were screened for all of the bacteriophages (complete and partial) assembled in this study (4,301). In total, 160 bacteriophages were present in more than 20% of the individuals, and the percentages of individuals that harbor them in each cohort are represented as a heat map. Each line of the heat map represents a virus.

Fig. 1.

Heat map indicating the presence of the 72 complete bacteriophage genomes in the globally distributed 62 healthy individuals represented in the Norman dataset (7). The percentage of healthy individuals from three global locations (Boston, Cambridge, Chicago) that harbor each of the complete bacteriophage genomes is indicated. Nine bacteriophages, including crAssphage (bacteriophage 31), were present in >50% of the individuals (core), and 46% were found in >20% of the individuals (core and common). Each line is a bacteriophage (phage).

Fig. S3.

Detection of HGP bacteriophage using increasing detection threshold. Core healthy gut phageome (HGP) bacteriophages were identified in individuals by read recruitment of high-quality deduplicated reads to bacteriophage contigs. If there was one read recruited, the virus was considered present in an individual. The percentage of individuals in which we could detect these bacteriophages using increasing detection thresholds (1 read versus 2, 5, 10, 50, or 100) is represented.

Fig. 2.

Reduction of the HGP present in IBD patients. (A) Comparison of percentage of healthy individuals (H) (n = 62) versus IBD-diseased individuals (CD and UC) (n = 102) that harbor each of the 23 core HGPs identified in this study. (B) Percentage of core, common, and unique bacteriophages (unique and low-overlap bacteriophages were pooled) present in all healthy and IBD individuals. Median is shown with a horizontal black bar. The number of core and common bacteriophages that IBD individuals harbor is significantly lower compared with healthy individuals. Significance was calculated using a Sidak’s multiple-comparison test with a 95% confidence interval.

Fig. 3.

Network-based analysis of the bacteriophage community in the human gut from two healthy individuals. (A) Graphical representation of the 44 network groups (colored by group) with greater than five contig membership. Each dot represents a contig. (B) Core groups (present in more than one-half of the individuals) are highlighted and labeled in red. (C) Heat map representing the percentage of individuals that have at least one member of each phage group. (D) Schematic organization of the bacteriophage community associated with the healthy gut microbiome.