2012
DOI: 10.1101/gr.138297.112
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CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

Abstract: 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 catal… Show more

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Cited by 189 publications
(215 citation statements)
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“…Most of the gut-residing phages we identified were targeted by CRISPR spacers extracted from gut microbiomes of multiple individuals. 28 This derived from mobile genetic elements, and further analysis confirmed most were of phage origin. In addition, a spacer match also revealed which prokaryotic species was infected by which phage, as the hosts harboring these spacers were known and spacers are derived from phages previously infecting the host.…”
Section: Holding a Grudgementioning
confidence: 99%
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“…Most of the gut-residing phages we identified were targeted by CRISPR spacers extracted from gut microbiomes of multiple individuals. 28 This derived from mobile genetic elements, and further analysis confirmed most were of phage origin. In addition, a spacer match also revealed which prokaryotic species was infected by which phage, as the hosts harboring these spacers were known and spacers are derived from phages previously infecting the host.…”
Section: Holding a Grudgementioning
confidence: 99%
“…1) have been used to study microbiomes in the ocean, 22,23 hot springs [24][25][26] and the human body. [27][28][29][30] There are yet more subtle ways in which CRISPR biology can inform on phagebacteria ecology. New spacer integrations in CRISPR arrays generally take place in a unidirectional manner next to a sequence element just upstream of the repeatspacer array ("leader"), as first inferred in Yersinia pestis and later verified experimentally.…”
Section: Holding a Grudgementioning
confidence: 99%
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“…Since the first viral metagenomic study was conducted in marine systems over a decade ago (Breitbart et al, 2002), the field has now expanded to include ecological studies of viral communities throughout the oceans globally, as well as diverse lakes and eukaryote-associated samples, including humans (Djikeng et al, 2009;Roux et al, 2012;Stern et al, 2012;Hannigan et al, 2015). Highlights of some of the ecological advances enabled by these studies include revealing…”
mentioning
confidence: 99%