The bacterial community in the human gut has crucial health roles both in metabolic functions and in protection against
pathogens. Phages, which are known to significantly affect microbial community composition in many ecological niches,
have the potential to impact the gut microbiota, yet thorough characterization of this relationship remains elusive. We
have reconstructed the content of the CRISPR bacterial immune system in the human gut microbiomes of 124 European
individuals and used it to identify a catalog of 991 phages targeted by CRISPR across all individuals. Our results show that
78% of these phages are shared among two or more individuals. Moreover, a significant fraction of phages found in our
study are shown to exist in fecal samples previously derived from American and Japanese individuals, identifying
a common reservoir of phages frequently associated with the human gut microbiome. We further inferred the bacterial
hosts for more than 130 such phages, enabling a detailed analysis of phage–bacteria interactions across the 124 individuals
by correlating patterns of phage abundance with bacterial abundance and resistance. A subset of phages demonstrated
preferred association with host genomes as lysogenized prophages, with highly increased abundance in specific individuals.
Overall, our results imply that phage–bacterial attack–resistance interactions occur within the human gut
microbiome, possibly affecting microbiota composition and human health. Our finding of global sharing of gut phages is
surprising in light of the extreme genetic diversity of phages found in other ecological niches.
[Supplemental material is available for this article.]
The bacterial community in the human gut has crucial health roles both in metabolic functions and in protection against
pathogens. Phages, which are known to significantly affect microbial community composition in many ecological niches,
have the potential to impact the gut microbiota, yet thorough characterization of this relationship remains elusive. We
have reconstructed the content of the CRISPR bacterial immune system in the human gut microbiomes of 124 European
individuals and used it to identify a catalog of 991 phages targeted by CRISPR across all individuals. Our results show that
78% of these phages are shared among two or more individuals. Moreover, a significant fraction of phages found in our
study are shown to exist in fecal samples previously derived from American and Japanese individuals, identifying
a common reservoir of phages frequently associated with the human gut microbiome. We further inferred the bacterial
hosts for more than 130 such phages, enabling a detailed analysis of phage–bacteria interactions across the 124 individuals
by correlating patterns of phage abundance with bacterial abundance and resistance. A subset of phages demonstrated
preferred association with host genomes as lysogenized prophages, with highly increased abundance in specific individuals.
Overall, our results imply that phage–bacterial attack–resistance interactions occur within the human gut
microbiome, possibly affecting microbiota composition and human health. Our finding of global sharing of gut phages is
surprising in light of the extreme genetic diversity of phages found in other ecological niches.
[Supplemental material is available for this article.]
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