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.

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

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“…Bacteriophages (phages) are estimated to be the most abundant organisms on earth, with key roles in shaping the composition of microbial ecology by lysing bacteria or transferring genes12. Despite the numerous available studies on DNA bacteriophages, the biology of RNA bacteriophages has been poorly investigated.…”

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“…[54][55][56] Yet outcomes from these studies suggest differing models of the roles of viruses and range of normal diversity. Some work suggests that there are components of a shared healthy virome, while others suggest that increased phage diversity was seen in patients with IBD.…”

“…Some work suggests that there are components of a shared healthy virome, while others suggest that increased phage diversity was seen in patients with IBD. 56,57 It bears mention that many of these viral sequence reads correspond to lysogenic and temperate phages, which could theoretically be harbored in bacteria in a manner that is challenging to describe as distinct from the bacterial microbiota. Further, these studies may provide more questions than answers in clarifying whether the role of phages is that of predator to prey, engine of genetic recombination and diversity generation, or still some other purpose.…”